Strange
Off the top of my head, maybe you originally purchased at least part of the game on account x, then played it on account y via game sharing and forgot.
Then when you got the S you logged on as account y and thus it didn't see your purchase history.
My understanding is the S isn't a new generation so things wouldn't need to be repurchased like it was form the 360-to-One
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I only kept one account though. I didn't share my xbox with anyone. I bought the standalone game when it was released, but they don't offer the standalone anymore, only the bundle. So I had to buy it again to play something other than a trial version.