Thanks for your investigation, and the tool!
After I got v1.1, I added, at line 78 (just after calculating penoffset and lastoffset), the following:
if datain[self.penoffset:self.penoffset+4] != 'SRCS':
raise StripException("already stripped")
The intention here is to not delete the FCIS segment from an already-stripped file (or one that was generated with -donotaddsource). I'm enough of a doofus that I'm sure to mess up something by stripping it twice! (On the other hand, I've found one source that says the FLIS and FCIS segments aren't necessary for the Kindle, so at least I'd get a few second chances.)