I have no idea what problems you are hitting or seeing, so I think that it’d be hard to offer much advice outside of long-shot guesses.
I’ve used xdelta, albeit not for GOG games, and didn’t know that they used xdelta for updates. I mean, it works, given a valid patch file and the right source file.
Are you sure that the source file is the correct version? What output are you seeing when trying to run xdelta?