The simplest method would be to verify game files. When you do this, steam deletes the proton prefixes and thus forcing to you reinstall the launcher on the next run, where you can then enable cloud saves. The only downside to this is that it takes time for your deck to scan through all the files to verify.

Alternatively you can also go to the proton folder for RDR2 in desktop mode and manually remove the folder that holds the rock-star launcher and game saves. This would be something like /home/deck/.local/steam/steamapps/common or something very similar to that. You would then find the folder for RDR2 which would be under its steam ID. I usually use protondb for looking this up. You can then delete or rename this folder and it will force steam to reinstall the launcher on the next run.

Warning: Both of these methods will delete the local copy of your save file. If you do not want these deleted, please back them up for attempting.

Got this setup and running on my Steam Deck. Really really cool. Love how clean it looks.

Yup same issue. It also prevents your unit from being able to shut down it seems like after launching a non-steam game. Hopefully something like this gets fixed fast.

Edit: ended up staying on main but switching to the stable branch. It corrected all the issues I was having currently.