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The Deck runs SteamOS which is a Linux. There's games offering native Linux builds which, subsequently, get ran on the Deck. However, there's also games not having cross-platform saves with the solution being to run the Windows version of a game on the Deck.
One game I remember people have reported to showcase this behavior is Hollow Knight, but there is others (I'm just too lazy to pump minutae into my head). So force the Windows build and see what happens.
If the developer keep the saves separate between the two OS's, there isn't much you can do. You either have to go back to using the native Linux version and never sync with the Windows version, or you forget you had a Linux save, force Proton and only use the Windows sync.
Which specific game is this for?
That game has had problems with their cloud saves long before the Steam Deck:
https://steamcommunity.com/app/203160/discussions/0/2143091512088359246/
https://steamcommunity.com/app/203160/discussions/0/540733524119456965/
https://steamcommunity.com/app/203160/discussions/0/1694914735995930666/