Can't speak for Jose, but for me it is very similar. Thread you mentioned starts with pre-/ postbuild steps, but in fact all of project custom settings (additional folders/includes/libraries etc.) are lost on *.ioc rebuild. That leads to errors building project (includes not found, etc.) Which is extremely frustrating. Actually it is hard to believe you did not encounter this problem in testing [you guys do testing, right? ;)].
My guess is CubeMX blindly recreates all project configuration files without regard to user changes. Which is obviously very wrong. Your workflow blindly implies that each and every change to the project came from CubeMX which is false as soon as you add one external library. I think you should at least warn user, that their custom changes will be lost on rebuild instead of silently deleting them.
