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I'm Lucy, and I'd be happy to answer your questions today.
The new owner cannot make you pay rent that has already been paid. If you have documentation showing that you made these payments to the prior owner when they were due (and before the current owner took ownership), then you do not have to pay anymore. He cannot evict you, charge you late fees, or otherwise take negative action against you, because your debt is paid. If the prior owner did not give him the excess rent that was collected over those 3 months, then the new owner needs to talk to him about that money. But it's not your responsibility - you paid, and you paid the right person the right amount.
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