Debugging Vds exceeded in motor drive application
Starter for 10:

Your explanation of what you think the error messages mean does not match what I would understand from them. You may have some reason to interpret them as you do but, if so, you should probably tell us.

High side FET gate drive voltages, which I take to be what they mean by "Bootstrap Voltages" are provided by diode pumps driven via C18, C19, C20 which are provided as  as the relevant low side FET switches from on to off, carrying the low side of each cap from near ground to near VIN (VN?) = VBB and the top of the cap to about VDD higher. I take the lack of bootsrap voltage to mean that there is a failure in this system in some manner. This can be due to lack of switching speed, lack of enough duty cycle, dead cap, dead IC and a few more things that Murphy can think of. 

Being built as your circuit diagram actually shows is one more such thing!!! (or I need more sleep, which I do, so I may have missed a connection, but I don't think so).

NB - if your diagram is to be believed, bootstrap cap B appears to be wrongly connected and so do Q2 and Q5. This is such a severe error that it seems more likely to be a "drafting/draughting/drawing/where did the dot go on the interscetion with Cage-V" error. ie an example of naughty drawing practices. If it's really wired like this then the last motor did well to run. 



Vds exceeded on A side low FET means just that - I'd have thought. It says that pin 34 = SA on the IC is being overvoltaged. How it knows this or if it is correct is TBD. If your motor phases produce double voltage on phases which are off under certain switching conditions then this may be what it means. 

This may be the datasheet for your IC - if not then a link to the correct one would be  agood idea [tm].

http://www.allegromicro.com/en/Products/Part_Numbers/4935/4935.pdf

Vbb_max = 50V so I'd imagine that exceeding that may generate the message. Or not. If the motor acts as a transformer then thsi MAY occur for Vbb > 25V or so.

What is the Vbb/ motor drive voltage?