@dc42 After a bit of trial and error I managed to get the toolboard to communicate with the mainboard again. What worked in the end was:
Setting up the Duet3 MB6HC board in standalone mode (latest 3.4b)
That gave me the DWC Error you mentioned about the toolboard trying to update (missing firmware)
However the TB still didn't respond to CAN commands even after factory resetting (with TB firmware 3.3 or 3.4b in the firmware folder)
reverting the MB6HC back to 3.3
TB installed the 3.3 firmware from MB
Updating TB to 3.4b
Updating MB to 3.4b
Something with the shipping firmware of the toolboard (3.2.2 IIRC) and the 3.4b seems to break communication after a firmware upgrade. I hope this helps.