the broker is going to send the covered cost basis data to the IRS; the non-covered cost basis data is not set to the IRS. Why change what the IRS is going to have?
you can adjust the cost basis of the non-covered sales to match your records since nothing is sent to the IRS and you would want the correct cost basis to correctly reflect you gain.
if you are saying the covered sales are correct without consideration of the non-covered sales, then I'd let it be.
