Manual saves are being deleted by the game for some reason. Only the 4 most recent saves are being retained. Two of them being auto-saves which are incorrectly marked as Manual Saves. I still have saves from 2017, but Beta 1.0 is deleting (or rather, overwriting) only between 4 save slots from newer versions of the save, even if you save manually or quick save.
I was doing a 100% achievement run for the new achievements with Hidden Hat, Pizza and Gas Cylinder, but I lost the saves