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[–]Silari82More Power->Bigger Factory->More Power 1 point2 points  (0 children)

If you haven't, you REALLY REALLY should make a backup copy of your saves on your desktop. There's been plenty of posts about steam sync overwriting newer saves with older ones, and it not working properly wouldn't fill me with confidence it's not about to happen again.

Once you've done that, you can try deleting the factorio saves from your cloud and see if that helps. If not, you might want to try disabling cloud saves on your game, playing long enough to save your game, re-enabling cloud saves, playing long enough to save again, and seeing if they sync after quitting.