(Hi. Just wanted to say that I have the same problem. The GoG downloader dowloaded the latest patch and when I entered the game I noticed that all my saves were gone. I guess threre's not much that can be done my saves, but you should warn other users to copy their saves before downloading the patch. )
p.s. Actually, never mind. I started the game again with the gog downloader turned on. And the saves were there again. Maybe others should try that too.