I'm reporting on behalf of a friend who is playing this on GOG. He says that GOG Connect was having trouble opening the game in the first place. He restarted it, but that didn't work. So he started the game from the exe file, and that was when he found that his saves were gone. He tried to reinstall GOG Connect, that didn't work, but it seems to be working fine. At some point during all of this, the cloud save feature overwrote his saves.

His machine is an HP desktop (about 8 years old; I'm looking for more stats) with Windows 7. The game plays really well. This save thing is the only problem.

Hope this helps.