I don't know, this needs to be tested. How exactly FPCUpDeluxe manages files in the repository. But it's likely that it uses git and some kind of non-destructive method, so most likely, if the changes were committed to git, then it's possible. But I repeat, this is just my assumption of reasonable behavior, as I don't actually know.
After the first build through FPCUpDeluxe, I switch completely to manual repository management. So far, everything has worked out, although I don't experiment that much.