Want to finish off this game having previously played it from a copy I bought on Desura but while I still have the save file I've changed computers since then and no longer have that copy installed. I also have the game from GOG now and I'd prefer to download/play that copy and I hope the save files will transfer over. Is anyone sure one way or the other if they will? I assume no major changes have been made between the two versions.

That's my assumption, too. I'm pretty sure they'll work. If you already own the GOG version, just give it a try.

I don't have the game on GOG, but on Desura it shows as version 1.0. AFAIK GOG version is 1.1, and I read that saves between those 2 versions are not compatible.

If you want, you can post your savegame here, some of us who own a GOG copy would be perfectly willing to try it out for you.