in part this may depend on what method the broker had you registered for if securities were sold. they may have you down for First-In, First, Out. In order to use a different method for any sale you would have to contact them before the sale to identify the lots you are selling. You need to contact them to discuss this matter.
just changing the cost on your schedule D/form 8949 might not work. the IRS will notice the mismatch (they get a copy of the 1099-B), recompute your taxes and send you a bill. if after 4/15, then there will also be penalties and interest.
there is code B for the form 8949 to use if the wrong tax basis is reported, but if you failed the follow the rules, the correct tax basis was reported.
