Not sure if this will help anyone else, but I couldn't find anything online about this and thought I'd share this with online just in case!
I just started playing Outer Wilds on the steam deck for a week or so, and was immediately in love with it. I decided to install it on my PC (popOS) to see how it looks with cranked graphics, and I could not for the life of me figure out how to sync my cloud saves! For some reason the deck kept saying the saves were syncing fine up to the cloud, but my pc kept sticking at 'checking....' when I asked it to sync...
In the end, I ended up finding a setting in the steam client that enables compatibility for every title in steam that isn't Linux native... when I flipped it on, Outer Wilds (along with like 4 other games in my library) all immediately resolved their bugged cloud sync!
So, I guess, steam will complain that it can't get your cloud saves to download, when really it doesn't have a compatdata folder for the saves to download to. Kinda jank!
I found it myself, Note that if you're on a Steam Deck (like I am), you'll need to go to desktop mode.
Thank you! I've been away from my PC for a bit, been meaning to come update this thread. This is the exact setting I changed! Both need to be ticked, & I selected proton experimental. I'm sure if experimental doesn't run it you can change per-game overrides to get it sorted out - steamDB can be your friend figuring out which version to use!