I have a similar problem.
I've found that if you switch to the transactions screen and have your managers determine your lineups and organization, your players mysteriously reappear.
Its annoying, but not world-shattering unless the AI decides to dump a player you were hanging on to for some reason that it thinks should go away.
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I'm a lifelong Phillies fan - "Hey, at least we beat the Braves in '93."
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