No, it's perfectly acceptable to enter two 1099-B transactions (covered, non-covered) summarizing the info. Check the box 'cost basis is missing or incorrect' and enter the correct basis calculated from your K-1 worksheet.
Enter 0's for the sale when entering your K-1, as you're reporting it as capital gains on the 1099-B, and don't want to be double-taxed.
Here's more discussion on Final K-1 Sale and 1099-B and How to Report Sale of PTP in TurboTax.
@icefyre123
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