Before launching the game, please consider backing up your save files. They are located here:
Win: %appdata%\Roaming\fates_of_ort\
Mac: ~/Library/Application Support/fates_of_ort/
Linux: ~/.config/fates_of_ort/
You can also see and download all saves associated with your account here:
https://store.steampowered.com/account/remotestorageapp/?appid=895480
If you receive a prompt about a save file conflict, be very careful about which file you choose.
FORCING A SYNC FROM PC TO STEAM DECK
On your Steam Deck:
Settings -> Properties... -> Compatibility -> tick "Force the use of a specific Steam Play compatibility tool"
Leave setting as "Proton Experimental"
Apply update
Launch the game (it will likely not run)
Settings -> Properties... -> Compatibility -> untick "Force the use of a specific Steam Play compatibility tool"
Apply update
Launch the game