The last App Store update was to fix a compatibility issue with the Steam and GOG versions of the game, caused by more recent data accidentally being included in the App Store build for the previous update, compared to the other versions.
Unfortunately, that data can effect saves, resulting in the error you mentioned. Older saves should be fine (before the previous game update, if available, though that was a while ago), or your recent saves should load properly after the next game update (currently being prepared, so there is no ETA yet).