DC_vipeout: The achievements are not directly related to the save game files. A call to GOG Galaxy client is issued at the moment you do the thing required for given achievement. You can delete the saved games, they will not change that. However, if you do not have an internet connection, this call is not immediately processed, rather "stored" in the client. Once you connect again, the client will sync and the achievement unlock will properly register with the servers.

There is another case though, and might be yours. If you are playing without the client, then we are responsible for storing the achievement data for later unlock. We store that data in the AncPlayerProfile.sav. That file is in the exact same folder as the saved games. So if you removed all files from the saved games folder, then you removed the profile also, and so the information about those achievements have been lost completely. I can only guess, that this is what happened to you as there is no way of confirming since all files that could tell us anything have been deleted :/