The issue from how I understand it is whenever you exit the game while the Deck is disconnected from the internet it will fail to sync save files. Then when it regains connection, instead of uploading the most recent file it has it downloads whatever it last put on the cloud and loads that instead. This is quite troublesome for a portable device.

However there is a way to fix this. Spyro Reignited saves the game in two different locations, one of which isn't ever synced to the cloud and is kept local on the Deck and one which is and is also usually loaded by the game. The solution is to replace the cloud one with the local one.

You will have go into desktop mode in order to preform this fix

Once in desktop mode you will want to open the file searcher dolphin, click on the little 3 line drop menu on the right and check Show Hidden Files

After that you'll wanna navigate to the first file location at:
>Home/.local/share/Steam/steamapps/compatdata/996580/pfx/drive_c/users/steamuser/AppData/Local/Falcon/Saved/SaveGames/FalconSave.106.sav

Copy the file above (And make a backup in case something goes wrong) then navigate to the second location:
>Home/.steam/steam/userdata/<user id number>/996580/remote/Falcon/Saved/SaveGames/FalconSave.106.sav

paste the first file into this location and replace it.

That's it. Once you return to gaming mode and launch the game your original save file should be back to how it was.
It will give you a save file out of sync warning before launching but just ignore it.
Make sure you're connected to internet before exiting the game again to ensure the save syncs properly.

Credit to Tesfallout who posted this solution but for windows PC's which I used as reference to find the Steam Deck equivalent