Michael Armani, aka Marmani on the Discord channels responded to the conversation with a point that I did not know, and is not mentioned on the Troubleshooting guide.
If using the Duet instructions for SAM-BA.
(https://duet3d.dozuki.com/Wiki/Installing_and_Updating_Firmware#Section_Fallback_procedure_Num_3)
Please DO NOT select at91sam4e8.
-That describes the Duet Wifi, not the Maestro.
Instead choose ATSAM4s8.
However, we do not use this tool and strongly recommend using Bossa instead. Please see our repair instructions https://coda.io/d/M3D-Public_dzE73kMbIAL/Duet-Maestro_sui8n#Cards_tubJG/r1, I would say at least 50% of the time we recover a board with funky behavior (No usb response, SD card reading, even sometimes a stuck pin). Updating the firmware helps with these, and sometimes the board just needs a refresh.