Are you using the standalone installer or GOG Galaxy, as it allows for cloud saves? The game, of course, shouldn't delete save files but there have been some fringe cases where people have indeed lost their save game. This usually happens in cases where the game is shut off or crashes during saving. For this reason there is the backup save system, but as you mentioned the backup saves seem to be quite old. You did try to rename the backup saves (both .bin and .xml file) from backup-profile.bin & xml to just profile.bin & xml and check of they work?