The System Shock remake is getting a massive patch with a revised ending, choice of female player character '8 years in the making', and a significant quality of life improvement
That's probably on Steam, not Nightdive? After all it's just uploading some files and downloading them again, something the steam client is supposed to do for you.
Nope, it's a bug with how Nightdive coded the save path. Since they made a native Linux version of the game, Steam is using that as opposed to doing Proton compatibility. So that means the save paths in the Linux version and the Windows version aren't the same, hence not syncing properly.
Cloud saves work fine between Linux PCs, but the devs seem to have misconfigured the save path for Steam cloud saves integration on Windows. That's why it doesn't work. That's on the devs, not the Steam client. Apparently they were working on a fix since about half a year ago, maybe they finally released that fix now?