Proton had a bug that deleted all Steam Cloud saves made on Windows for any game I launched it with. Not sure if it is fixed yet because I'm scared to try again. Beware & make backups
fyi you can directly view and download the saves and config files that get uploaded to the steam cloud. you could always download them as a backup before launching the game. it would not surprise me if there were oss tools to help manage that as well
https://store.steampowered.com/account/remotestorage