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Only if they implement steam cloud saves. Its not automatic.

Dolphin's Twitter account stated that cloud saves was part of the Steam release.

It really is one of the main reasons to do a Steam release. Seamlessly playing your savegames and save states on desktop PC over to Steam Deck and back again made RetroArch one of the killer Deck apps IMO.

Even without Steam, you could use Syncthing for your Dolphin-emu data.

Or even an ftp server and rsync.

It's pretty close though, there's a mode where you can just point Steam Cloud at a folder and it will sync it.

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