With the save file, you'll probably overwrite it with a re-install, as I don't think GOG separates out expansions from the game at instillation (And you'd be reinstalling the game too), unless it's something like Starcraft: Broodwar where the expansion was a whole different game (Which if it was separate from the original, would require a new save anyway). If you want to hang onto it, you'll need to pull the save files into another folder while the old version overwrites, and re-insert them into the new save folder. But then, that may not always work. Also, your saves may not be compatible with the upgrade, meaning it doesn't do any good anyway. Most of the time developers are good about backwards compatible software. For example, The Elder Scrolls 3, you could install both expansion packs whenever you want, any time you want, regardless of how far you were. One map is impossible to reach by foot, the other is far from the mainland, but if you're determined you can swim. Or you can take the boat like a normal person. But neither existed on the original game

Hopefully that gives you a couple of ideas what to expect.