Environment
Steam Cloud used on a desktop and Steam Deck.
What happens
Progress made on the desktop disappears after launching the game on the handheld.
What I have tried
Verified that both devices show cloud synchronization as complete.
I would appreciate advice on how to identify the root cause without risking existing data or configuration.
Verified community troubleshooting
The important clue is that the problem only appears under the conditions you described.
Likely cause: One device uploads an older save after its clock or sync metadata becomes inconsistent.
What I would try: Back up both save folders, disable cloud sync temporarily, keep the newest local save and re-enable sync from that device first.
Avoid applying several fixes at once, otherwise it will be difficult to know which one mattered.
I can reproduce it consistently, so I should be able to confirm whether this solves the root cause.