The game is installed on Pop!_OS, ext4 file system. Windows came, so proton has the save games in a weird spot. I did notice it’s different than the location of steam deck.
Pop!_OS: ~/.steam/steam/steamapps/compatdata/1091500/pfx/drive_c/steamuser/Saved Games/CD Projekt Red/Cyberpunk 2077
Steam Deck: ~/.local/share/Steam/steamapps/compatdata/pfx/drive_c/users/steamuser/Saved Games/CD Projekt Red/Cyberpunk 2077
What’s weird is that it synchronized at least some saves form early in the game. But now it is continually failing to sync. I fired up a few indie games just last night and those synchronized just fine. Fates of Ort and Void Scrapper, if it matters ;)