Just for anyone who is experiencing this or for the curious:
** This is for a Gotek HxC, not sure if it applies with the standard HxC or not... **
If you set the HFE interface type to Emu Shugart then it corrupts the entire HFE if there's a write error. If the HFE is set to Generic Shugart then even if there's a write error you can attempt to re-write multiple times until it works and there is no damage done to the HFE.
I'm sharing this mostly because one might assume that an E-mu product would require (or work best with) an Emu Interface setting, but this doesn't seem to be the case.