Sadly, from what I know... GOG patching is utter and utter crap.
Somewhat explainable being for old games who wouldn't need any more patching again, but still.
Apparently their Galaxy will fix it in... August/September?
For now you just have to rely on 'updated' in your GOG library and re-downloading the entire game each time yeah. It's definitely not fun, but nothing Larian can do about that, that's GOG's system
(And yes, usually it's behind on Steam patching by some time... making Steam/GOG compatibility difficult if you were planning on that. Should become easier once less, but bigger patches come out)
