I haven't seen this adressed, so forgive me if this has already been covered elsewhere. I would like to share the method I've figured out to recover your progress when the game glitches and reverts your progress.

The issue, as far as I can tell, stems from the fact the Spyro Reignited Trilogy saves your data in 2 separate places that don't always agree with each other.

The first save file, and the one that always (at least in my experience) seems to be correct is located at
C:\Users\<User>\AppData\Local\Falcon\Saved\SaveGames\FalconSave.106.sav

and the second save, which also happens to be the one the game actually loads on startup is located at
C:\Program Files (x86)\Steam\userdata\<user ID>\996580\remote\Falcon\Saved\SaveGames\FalconSave.106.sav

Once you have found both locations, the fix is simple. Simply copy and paste the save data from the AppData directory and overwrite the data in the Steam directory. It may not be a bad idea to change the name of the original file to make a backup before doing this.

If all goes well, on your next startup, you will have your save data back. I hope this helps, please let me know if I missed anything.