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As I went digging around to see if I could tlrsync them across, I found them, and managed to continue playing... but now I have to manually do this every time...
But then I noticed just now... it is likely due to the Steam Deck installing the Windows version instead of the Native one! They save data in different directories...
I wonder why they would have done this. I don't see a way to switch back either, as it seems usually you use native or force compatibility to Proton, but that is unchecked.
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But think from this perspective. If there is indeed a case where Cloud Saves only work with the like-install. It makes more sense that they'd think people would be playing on Windows on their computers, and so it would make sense to install the Windows version on the Deck.
Then again, it makes more sense to create a symlink, so that it wouldn't matter... Trying to decide if this is an issue with the developer, or should be reported to Valve. I'm thinking the latter.
Wonder if Liam has ran into this.