Hi James,
in principle, no derived/generated files should be stored in a version control system:
Version Control with Processor Expert Projects | MCU on Eclipse
It's like not storing object files in a version control system too.
The above article outlines the aspects. But I agree that the .pe file itself is very problematic to be used in a VCS.
In case you really want to store the generated sources: you could disable code generation of modules, see Disable my Code Generation | MCU on Eclipse.
The other thing are the *.g_x and *.g_c files: they store information about the code generation. Not sure if you store them in your VCS or not (I do not).
Otherwise, if you do any change of the .pe file, this can trigger a code generation. There is as well a global preference to prevent automatic code generation (see above article).
As a last note: the next version 10.5 has scheduled improvements in this area, so things should be improved.
In any case, if you get a code generation like you describe without having touched the .pe file, the *.g_x or the *.g_c, then I consider this as a bug. If this is the case, I would appreciate if we can submit that to the engineers as having Processor Expert working with a VCS is a big topic for me: I run classes with students and they all share their sources in GIT, so everything which makes this easier for us will help everyone else :-)
Erich