So on your Schedule D used in the return to report the sale of stocks and mutual funds there is a section for both long-term and Short-term sales. in each of these sections there is a further breakout of 3 more sections. these are marked A - F (ABC shorth-term & DEF long-term)
For your situation go back to Quicken and change the basis from average to specific lot. You will then need to identify the shares you sold where the basis is not reported and use the basis in Quicken for those shares.
Option 2 depending on the total amount of transactions (4, 12, 50 or more) the dollar amount ( $200 or 2,000, or $200,000 or more) and your capital gain rate (0% or more) you may want to see a tax professional to review your investments reporting. If you are in the 0% capital gain tax rate it may not worth even filing an amended return. Or if its a lot of money and capital gains it may be well worth talking to a tax professional to set up how to record and report capital gains in the future.
