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I assume you rented out the other unit over time, and are selling the portion of the dwelling that you have lived in as a principal residence. The first sale should qualify for the exclusion.
When you move into the other unit, and live in it for the qualifying two years of five as your new principal residence, you can exclude the second gain as well, as adjusted for some depreciation recapture that might be needed (when it was a rental apartment).
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