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I have seen cases of EA deleting entire save directories. I am guessing that what has happened is, in order to get games working again on the steam deck, rather than update the EA app which is causing the problems, EA have pushed out a reinstall of the entire prefix (the simulated windows environment that the game runs in). I often have to do this manually after EA update their app, just to get things working, but of course, I back up my saves first!! It's a really lazy fix that actually fixes nothing and shows complete contempt for users, if that's what they've done.