The game keeps the most recent autosave and most recent manual save. It should automatically use the more recent of the two when you load a saved game. You can choose which of the two to load once the game loads (under the Options menu).

If both of those are quite old then sadly there's no way to recover the lost progress that I'm aware of.

Do you have online saves enabled? Although primarily reported on Steam there have been known problems with online saves not being fully updated and reverting to older saves and it may be that this can happen with GOG. Suggest disabling online saves. If using the GOG Galaxy click the Settings gear in upper left, then click Settings, then click Game features and finally unclick Cloud Saves.

Another thing to do is to make manual backups of saves for times when something just does not work out correct such as going to another system or selecting the wrong option.

Sounds like a cloud save issue - do you use that?