I'm about to buy a SKR 3, hopefully this will solve the original issue that started this thread. If it still keeps on disconnecting, I'll buy a new cable or replace the original wires that it came with and hopefully that will be the end of it.

I finally installed a esp32 from btt and it works just fine. Too bad I couldn't find an answer for the original question that started this thread. I might revisit this at some point in the future, who knows...

Small update regarding modifying uart drivers:

DON'T DO IT YET

I have been getting constant short to vin / short to ground errors ever since installing the EZ drivers and the modified 2209's. I have tried the following setups:

• only EZ drivers: getting random short to vin errors (with no apparent cause), still able to move motors
• EZ and modified drivers: getting random short to vin errors on EZ drivers (with no apparent cause), still able to move motors; getting short to vin errors when trying to move motor connected to driver
• only modified drivers: getting short to vin errors when trying to move motor connected to driver
• only stock drivers: everything works fine

Before anyone asks, I can confirm that the issue isn't with the wiring or motors, since the error message would appear on the EZ drivers even when the motors or cables weren't connected to the board. Using 24v or 48v didn't do a difference.

I have contacted btt support and waiting for an answer. If I don't receieve anything useful in the following days, I will buy a new board with 2209 EZ drivers for troubleshootind purposes, as I can't rule out my board being the issue; considering that I have a nonfunctional driver slot there might be other issues with it that I don't know.

I will keep you updated when I will get a response / receive the new board.

I have edited the coordinates for probing and now it behaves as it should. However, I keep on getting the following error:

Error: Some computed corrections exceed configured limit of 1.00mm: 2.404 -2.621

Can I increase the configured limit?

edit: nevermind, I figured it out (it's the S parameter in M671). Probing works as it should now.

@droftarts Yes, the probe is to the left and in front of the nozzle

@droftarts I am also trying to probe at the min. edge of the x axis, however the printhead stops about 20-30mm from the edge. Am I supposed to subtract the offset from both probing coordinates?
When I specify x and y, are those the coordinates for the printhead or bltouch?

I am trying to get G32 working for my printer in order to compensate for what i suspect is a slightly twisted x axis (my bed meshes always come at an angle despite manual leveling). I followed the instructions from https://docs.duet3d.com/en/User_manual/Connecting_hardware/Z_probe_auto_levelling . However, upon sending G32, the printhead probes at about 50mm near the first leadscrew, and then it crashes into the axis limit trying to reach the second leadscrew.

Here are the config and bed files:

; Configuration file for BTT SKR 3 EZ (firmware version 3)
; executed by the firmware on start-up

; General preferences

G4 S2                                          ; wait 2 seconds

M669 K1                                        ; select CoreXY mode

G90                                            ; send absolute coordinates...
M83                                            ; ...but relative extruder moves
M550 P"My Printer"                             ; set printer name

; Network
M552 S1                                        ; enable network
M586 P0 S1                                     ; enable HTTP
M586 P1 S0                                     ; disable FTP
;M586 P2 S0                                     ; disable Telnet                                      

; Drives
M569 P0 S1 D2                                    ; physical drive 0 goes forwards using default driver timings
M569 P1 S1 D2                                    ; physical drive 1 goes forwards using default driver timings
M569 P2 S0 D2                                  ; physical drive 2 goes forwards using default driver timings
M569 P3 S0 D2                                   ; physical drive 3 goes forwards using default driver timings
M569 P124.0 S1				       ; physical drive 124.4 goes forwards using default driver timings
M584 X0 Y1 Z2:3 E124.0                              ; set drive mapping
M350 E256 I0                              ; configure microstepping with interpolation
M350 X16 Y16 Z32 I1                                ; configure microstepping with interpolation
M92 X80.00 Y80.00 Z800.00 E6501         ; set steps per mm
M566 X900.00 Y900.00 Z200.00 E1200.00           ; set maximum instantaneous speed changes (mm/min)
M203 X30000.00 Y30000.00 Z1000.00 E3000.00        ; set maximum speeds (mm/min)
M201 X15000.00 Y15000.00 Z500.00 E5000.00         ; set accelerations (mm/s^2)
M906 X1000 Y1000 Z800 E800 I5                  ; set motor currents (mA) and motor idle factor in per cent
M84 S30                                       ; Set idle timeout

;M556 S1 X-0.0036843

; Axis Limits
M208 X0 Y0 Z0 S1                               ; set axis minima
M208 X265 Y280 Z290 S0                         ; set axis maxima

; Endstops
M574 X2 S1 P"e0stop"                            ; configure switch-type (e.g. microswitch) endstop for high end on X via pin xstop
M574 Y2 S1 P"e1stop"                            ; configure switch-type (e.g. microswitch) endstop for high end on Y via pin ystop
M574 Z1 S2                                     ; configure Z-probe endstop for low end on Z

; Z-Probe
M950 S0 C"124.io0.out"                              ; create servo pin 0 for BLTouch
M558 P9 H5 F250:60 T8000 C"124.io0.in"                ; set Z probe type to bltouch and the dive height + speeds
G31 P500 X-22.345 Y-6.941 Z0.689                            ; set Z probe trigger value, offset and trigger height
M557 X15:215 Y15:215 S50                       ; define mesh grid
M671 X-22:287 Y163:163

; Heaters
M308 S0 P"bedtemp" Y"thermistor" T100000 B4092 ; configure sensor 0 as thermistor on pin bedtemp
M950 H0 C"bed" T0                              ; create bed heater output on bed and map it to sensor 0
M307 H0 B0 S1.00                               ; disable bang-bang mode for the bed heater and set PWM limit
M140 H0                                        ; map heated bed to heater 0
M307 H0 R0.320 K0.414:0.000 D1.01 E1.35 S1.00 B0 V24.6 ; set PID values for heated bed
M143 H0 S130                                   ; set temperature limit for heater 0 to 120C
M308 S1 P"124.temp0" Y"thermistor" T100000 B4092  ; configure sensor 1 as thermistor on pin e0temp
M950 H1 C"124.out0" T1                           ; create nozzle heater output on e0heat and map it to sensor 1
M307 H1 B0 S1.00                               ; disable bang-bang mode for heater  and set PWM limit
M143 H1 S300                                   ; set temperature limit for heater 1 to 300C
M307 H1 R3.201 K0.662:0.000 D9.07 E1.35 S1.00 B0 V24.0 ; set PID values for heater 1

; Fans
M950 F0 C"124.out2" Q250                           ; create fan 0 on pin fan0 and set its frequency
M106 P0 S0 H-1                           	   ; set fan 0 value. Thermostatic control is turned off
M950 F1 C"124.out1" Q500                           ; create fan 1 on pin fan1 and set its frequency
M106 P1 S0 H1 T100                                 ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0                               ; define tool 0
G10 P0 X0 Y0 Z0                                ; set tool 0 axis offsets
G10 P0 R0 S0                                   ; set initial tool 0 active and standby temperatures to 0C
T0                                             ; select first tool

; TFT Screen
;M575 P1 S0 B115200				; enable support for tft

; Miscellaneous
M955 P124.0 I10 
M572 D0 S0.035
M912 P0 S-8.9

M593 P"zvdd" F41 ; use ZVDD input shaping to cancel ringing at 41Hz

M308 S2 Y"drivers" A"DRIVERS"  			; configure sensor 2 as temperature warning and overheat flags on the TMC2660 on Duet
M308 S3 Y"mcu-temp" A"MCU" 			; configure sensor 3 as on-chip MCU temperature sensor
M308 S4 Y"thermistor" P"124.temp1" A"RRF_36" T100000 B4092	; configure sensor 4 as temperature sensor on RRF36 CAN-FD board
M950 F2 C"fan2" Q20000 				; create fan 2 on pin fan2 and set its frequency
M106 P2 H2:3 L0.15 X0.65 B0.3 T40 		; set fan 2 value

M501	

; bed.g
; called to perform automatic bed compensation via G32
;
; generated by RepRapFirmware Configuration Tool v3.4.0-LPC-STM32+7 on Sun Aug 20 2023 12:46:47 GMT+0300 (Eastern European Summer Time)
M561 ; clear any bed transform
G28 ; home
while true
    G30 P0 X0 Y140 Z-99999 ; probe near a leadscrew, half way along Y axis
    G30 P1 X265 Y140 Z-99999 S2 ; probe near a leadscrew and calibrate 2 motors
    if abs(move.calibration.initial.deviation) < 0.01 || iterations > 3
        break

I can confirm that the issue only appears when running drivers in stealthchop, no mather the speed. Sitting at idle with stealthchop on 5160's is enough to summon short to vin errors, while 2209's will throw an error only before a random move.

I might have figured it out:
When I first installed 5160 drivers I noticed that the steppers were pretty loud even at standstill, at which point I realised that I was using spreadcycle on all drivers; after which I changed it all to stealthchop.

Well, I am currently runing a print job (with no filament, just to see if the movement is ok) with 2209's in spreadcycle, and now it's working again just like before.

Does anyone know why changing from stealthchop to spreadcycle would fix the issue?

I will try 5160's in spreadcycle after the print finishes to confirm that this is the issue.

Update:
New board and 2209 EZ drivers arrived. I tried some basic tests (homing and m122 output) with both ez and modified stepstick drivers. As soon as I tried 5160's, I received a short to vin error, leading me to think that I got sent faulty drivers. As for the stock and modified 2209's, I don't think they are damaged. More testing to come, I still need to finish a print first in order to give the green light to cutting the pins on a stepstick driver.

I also received a reply from biqu support regarding the skr 3 ez board, saying that I might have damaged the board with static electricity, short circuits or wiring errors.

edit: there was a small glitch that almost made my heart stop where after plugging in a 2209 in the slot where there was previously a 5160, the slot would become unresponsive, and I had to powercycle the board and change the order of the drivers a few times in order to make it working again.

2nd edit: I am now thinking that I just caused the same error on this brand new board aswell. I started receieving short to vin errors again on all ez drivers. Just great.

@gloomyandy 100% sure they weren't super with 48v.

I guess I will buy a new board with drivers. Ironically, it is cheaper to buy the board with 5 EZ 2209's then just the board itself on aliexpress. I can test if the problem is with the old board or not when it arrives.

@gloomyandy Yes, when I revert back to 2209's I still get errors. And yes, in test one I only had 5160 drivers installed.

I modified board.tx with stepper.DriverType = {unknown,unknown,TMC2209,TMC5160,TMC5160}, hoping that it would solve the issue. It didn't.

Here is the output of m122 after turning on the printer and waiting for a couple minutes (I did receive a short error in the meantime for driver 3):

m122
=== Diagnostics ===
RepRapFirmware for STM32H7 based Boards (skr3_h743) version 3.5.3 (2024-09-18 20:53:33) running on STM32H743 (standalone mode)
Board ID: H10W1-0W0K2-D6MW8-6PTFW-GGLWV-70000
Used output buffers: 3 of 40 (36 max)
=== RTOS ===
Static ram: 48816
Dynamic ram: 109268 of which 1292 recycled
Never used RAM 251856, free system stack 151 words
Tasks: NETWORK(2,nWait 7,10.8%,244) HEAT(3,nWait 6,0.0%,371) Move(4,nWait 6,0.0%,339) CanReceiv(6,nWait 1,0.0%,300) CanSender(5,nWait 7,0.0%,336) CanClock(7,delaying,0.0%,332) TMC22xx(4,nWait 6,0.5%,133) TMC51xx(4,delaying,5.3%,157) FSWRITE(2,nWait 4,0.0%,561) MAIN(1,running,83.0%,113) IDLE(0,ready,0.3%,29), total 100.0%
Owned mutexes: WiFi(NETWORK) BITIO(TMC22xx)
=== Platform ===
Last reset 00:04:02 ago, cause: software
Last software reset at 2025-01-04 19:16, reason: User, Gcodes spinning, available RAM 248812, slot 1
Software reset code 0x0003 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x00400000 BFAR 0x00000000 SP 0x00000000 Task MAIN Freestk 0 n/a
Error status: 0x00
MCU temperature: min 41.2, current 41.4, max 50.1
Supply voltage: min 24.0, current 24.0, max 24.0, under voltage events: 0, over voltage events: 0, power good: yes
Heap OK, handles allocated/used 0/0, heap memory allocated/used/recyclable 0/0/0, gc cycles 0
Events: 1 queued, 1 completed
Driver 0: not present
Driver 1: not present
Driver 2: standstill 2209, SG min 2, reads 48287, writes 12, error r/w 0/1, ifcnt 46, timeout 0
Driver 3: standstill 5160, SG min n/a, mspos 824, reads 44919, writes 16
Driver 4: standstill 5160, SG min n/a, mspos 72, reads 44919, writes 16
Driver 5: 
Driver 6: 
Driver 7: 
Driver 8: 
Driver 9: 
Driver 10: 
Driver 11: 
Driver 12: 
Driver 13: 
Date/time: 2025-01-04 19:20:38
Slowest loop: 2.81ms; fastest: 0.05ms
=== Storage ===
Free file entries: 20
SD card 0 detected
SD card longest read time 1.7ms, write time 0.0ms, max retries 0
=== Move ===
DMs created 125, segments created 0, maxWait 0ms, bed compensation in use: none, height map offset 0.000, max steps late 0, min interval 0, bad calcs 0, ebfmin 0.00, ebfmax 0.00
no step interrupt scheduled
Moves shaped first try 0, on retry 0, too short 0, wrong shape 0, maybepossible 0
=== DDARing 0 ===
Scheduled moves 0, completed 0, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 0, 0], CDDA state -1
=== DDARing 1 ===
Scheduled moves 0, completed 0, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 0, 0], CDDA state -1
=== Heat ===
Bed heaters 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1, chamber heaters -1 -1 -1 -1, ordering errs 0
Heater 1 is on, I-accum = 0.0
=== GCodes ===
Movement locks held by null, null
HTTP is idle in state(s) 0
Telnet is idle in state(s) 0
File is idle in state(s) 0
USB is idle in state(s) 0
Aux is idle in state(s) 0
Trigger is idle in state(s) 0
Queue is idle in state(s) 0
LCD is idle in state(s) 0
SBC is idle in state(s) 0
Daemon is idle in state(s) 0
Aux2 is idle in state(s) 0
Autopause is idle in state(s) 0
File2 is idle in state(s) 0
Queue2 is idle in state(s) 0
Q0 segments left 0, axes/extruders owned 0x80000003
Code queue 0 is empty
Q1 segments left 0, axes/extruders owned 0x0000000
Code queue 1 is empty
=== CAN ===
Messages queued 2190, received 4848, lost 0, errs 0, boc 0
Longest wait 2ms for reply type 6053, peak Tx sync delay 204 free buffers 50 (min 49), ts 1209/1208/0
Tx timeouts 0,0,0,0,0,0
=== Network ===
Slowest loop: 43.89ms; fastest: 0.00ms
Responder states: MQTT(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0)
HTTP sessions: 1 of 8
Uploads/Errors: 0/0
=== WiFi ===
Interface state: active
Module is connected to access point 
Failed messages: pending 0, notrdy 0, noresp 0
Bad header: 0/0
Firmware version 2.1.0
MAC address 0c:dc:7e:9a:2d:10
Module reset reason: Power up, Vcc 0.00, flash size 4194304, free heap 188636
WiFi IP address 192.168.1.6
Signal strength -39dBm, channel 1, mode 802.11n, reconnections 0
Clock register 00003043
Socket states: 0 0 0 0 0 0 0 0

And here it is after trying to home the machine: X and Y homed ok, Z vibrated and was slowly dropping the bed while trying to raise it

m122
=== Diagnostics ===
RepRapFirmware for STM32H7 based Boards (skr3_h743) version 3.5.3 (2024-09-18 20:53:33) running on STM32H743 (standalone mode)
Board ID: H10W1-0W0K2-D6MW8-6PTFW-GGLWV-70000
Used output buffers: 18 of 40 (36 max)
=== RTOS ===
Static ram: 48816
Dynamic ram: 109300 of which 1260 recycled
Never used RAM 248788, free system stack 132 words
Tasks: NETWORK(2,nWait 7,10.4%,244) HEAT(3,nWait 6,0.0%,356) Move(4,nWait 6,0.0%,244) CanReceiv(6,nWait 1,0.0%,300) CanSender(5,nWait 7,0.0%,336) CanClock(7,delaying,0.0%,332) TMC22xx(4,delaying,0.5%,133) TMC51xx(4,delaying,5.4%,157) FSWRITE(2,nWait 4,0.0%,561) MAIN(1,running,83.7%,113) IDLE(0,ready,0.0%,29), total 100.0%
Owned mutexes: WiFi(NETWORK)
=== Platform ===
Last reset 00:08:29 ago, cause: software
Last software reset at 2025-01-04 19:16, reason: User, Gcodes spinning, available RAM 248812, slot 1
Software reset code 0x0003 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x00400000 BFAR 0x00000000 SP 0x00000000 Task MAIN Freestk 0 n/a
Error status: 0x00
MCU temperature: min 41.2, current 41.3, max 41.5
Supply voltage: min 24.0, current 24.0, max 24.0, under voltage events: 0, over voltage events: 0, power good: yes
Heap OK, handles allocated/used 99/0, heap memory allocated/used/recyclable 2048/16/16, gc cycles 0
Events: 2 queued, 2 completed
Driver 0: not present
Driver 1: not present
Driver 2: phase A short to Vin, standstill 2209, SG min 0, reads 53464, writes 2
Driver 3: standstill 5160, SG min 0, mspos 808, reads 5188, writes 3
Driver 4: standstill 5160, SG min 0, mspos 104, reads 5188, writes 3
Driver 5: 
Driver 6: 
Driver 7: 
Driver 8: 
Driver 9: 
Driver 10: 
Driver 11: 
Driver 12: 
Driver 13: 
Date/time: 2025-01-04 19:25:06
Slowest loop: 6.96ms; fastest: 0.05ms
=== Storage ===
Free file entries: 20
SD card 0 detected
SD card longest read time 1.7ms, write time 0.0ms, max retries 0
=== Move ===
DMs created 125, segments created 9, maxWait 494162ms, bed compensation in use: none, height map offset 0.000, max steps late 0, min interval 0, bad calcs 0, ebfmin 0.00, ebfmax 0.00
no step interrupt scheduled
Moves shaped first try 3, on retry 0, too short 0, wrong shape 4, maybepossible 0
=== DDARing 0 ===
Scheduled moves 12, completed 12, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 0, 0], CDDA state -1
=== DDARing 1 ===
Scheduled moves 0, completed 0, hiccups 0, stepErrors 0, LaErrors 0, Underruns [0, 0, 0], CDDA state -1
=== Heat ===
Bed heaters 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1, chamber heaters -1 -1 -1 -1, ordering errs 0
Heater 1 is on, I-accum = 0.0
=== GCodes ===
Movement locks held by null, null
HTTP is idle in state(s) 0
Telnet is idle in state(s) 0
File is idle in state(s) 0
USB is idle in state(s) 0
Aux is idle in state(s) 0
Trigger is idle in state(s) 0
Queue is idle in state(s) 0
LCD is idle in state(s) 0
SBC is idle in state(s) 0
Daemon is idle in state(s) 0
Aux2 is idle in state(s) 0
Autopause is idle in state(s) 0
File2 is idle in state(s) 0
Queue2 is idle in state(s) 0
Q0 segments left 0, axes/extruders owned 0x80000007
Code queue 0 is empty
Q1 segments left 0, axes/extruders owned 0x0000000
Code queue 1 is empty
=== CAN ===
Messages queued 2417, received 5364, lost 0, errs 0, boc 0
Longest wait 1ms for reply type 4012, peak Tx sync delay 6 free buffers 50 (min 49), ts 1337/1337/0
Tx timeouts 0,0,0,0,0,0
=== Network ===
Slowest loop: 20.58ms; fastest: 0.07ms
Responder states: MQTT(0) HTTP(2) HTTP(2) HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0)
HTTP sessions: 1 of 8
Uploads/Errors: 0/0
=== WiFi ===
Interface state: active
Module is connected to access point 
Failed messages: pending 0, notrdy 0, noresp 0
Bad header: 0/0
Firmware version 2.1.0
MAC address 0c:dc:7e:9a:2d:10
Module reset reason: Power up, Vcc 0.00, flash size 4194304, free heap 182500
WiFi IP address 192.168.1.6
Signal strength -41dBm, channel 1, mode 802.11n, reconnections 0
Clock register 00003043
Socket states: 0 5 0 0 0 0 0 0