When I'm playing GOG games on my Steam Deck via the shortcut made by Heroic, the autosync setting seems to be ignored. If I launch the game from Heroic itself it works exactly as it should, but not if I use the generated Steam shortcut and I instead have to go and manually upload/download my save files (which defeats the point of having the autosync enabled).
This wouldn't be such a big deal if Heroic itself wasn't difficult to navigate with a controller (namely getting to the next row of game in the list requires pressing down multiple time for it to actually start scrolling bit by bit).