Thanks to the information on this post we have successfully reproduced the issue and know what is causing the failure.
Essentially, if you are running the motors at a high RPM and then change direction quickly (as mentioned by @Vikram_Bansal) the voltage on the power rail will exceed the limit of the diode and cause it to fail. This is easy to replicate using voltage mode to control the motors. However it still may be possible in other modes as well.
We are testing a firmware fix now. But anytime we make a change to these motors we have to do a lot of testing to make sure we did not cause any other issues.
I hope to have more information for you tomorrow.