Yes, you can file separately for your wife to claim the rest of her stimulus payment. Filing separate in your situation may produce the best results when it comes to the stimulus refund.
You may want to do a mock return for both of you to see if the stimulus creates an actual benefit when you file separate. In your situation, it sounds like it is the best, but it doesn't hurt to enter her information and your information separate then add the amounts and compare to the amount you would receive if you file jointly.
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