say i download game 'X' play it and make several saves, then gog make a new version of the game to download and i download it and install it to the same place, what would happen to the game saves?

If you install new version of the game in the same place I think there should be no problem to use your old savegames. But to be 100% sure you can backup them elsewhere and put again back in the same place after fresh install.

I can't image GOG's game modifications affecting save games. Only exeption would be games that needed unofficial patches to work but those are pretty rare. Nor are GOG modifications usually big enough to warrant switching over mid game if your installed game is working well. I'd suggest finshing ongoing game before switching unless GOG reports that they fixed something game breaking.

If you still want to switch mid game, I'd suggest backing up the save games (also obviously uninstall before you install the new version as GOG does not provide patches so you can't really upgrade previous installation. Installing over existing game may wreak havoc on your registry.). I havent' uninstalled enough GOG games to know wether or not they allow preserving save games.

Check where your save games are, most games put them in a folder under My Documents. Some games put them under the game install directory, but then won't delete them even on uninstall unless you check the "remove all game data" (or similarly titled) checkbox. If you install right over the top of the old install you shouldn't get any deleted saves in either case (you could have patch or mod issues if the save files are altered due to specific mods or patch versions - if you didn't install mods and it's the same version disregard this).