It doesn't sound like like there is any double taxation here. The type and amount of gain or loss from the sale of business assets (in this case your rental property) is calculated on Form 4797. That gain or loss the flows to Form 8825 where rental property income, expenses, gains, and losses are reported. It is combined with those other items and then that number flows to the main form - 1065. I don't see where the gain is reported twice, based on your description.
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