I had a similar situation a couple of years ago. I had to keep a spreadsheet of all my RSUs because each had a different acquisition date and basis. So when I filed my taxes i adjusted the both the proceeds and cost amounts to match my spreadsheet. I think the important thing is that the total proceeds still needs to match your 1099 document so the IRS does not create a mismatch on their system. So you can add an additional sale to the 1099 to make the total proceeds match and adjust the costs accordingly with your spreadsheet. Just keep good records. I never got audited on this, but I felt ready if it happened.
To change both the cost and proceeds, you use the edit function (pencil icon) when reviewing the individual sales for each 1099. Down at the bottom of the 1099 review page, their is an option to add additional sales.
