One of my duties at ICLUBcentral is dealing with clubs whose records do not match the records of their broker. There has been some chatter about recent announcements of broker mergers and how this might affect the reconciliation of club and broker records. TDAmeritrade, Folio Investing and E*Trade are about to be acquired by other firms. Such mergers should not affect cost basis and gain calculations kept by your broker. Usually the information is consolidated into the acquiring firm's system with no changes. There may be some glitches though that cause the new firm to change cost basis and/or gain data for a club. What can you do to be prepared for such an event if it happens to you?
1.) Check your records against your current broker's data. If there are discrepancies can you explain them? (A spin-off or merger-with-cash in the company history are 2 possible reasons for legitimate differences due to differences in market value estimates in these transactions.)
2.) Do you have securities purchased before January 1,2011? Broker's were not required to track cost basis of securities purchased before that date. If your old broker did not track the cost basis of those purchases they may not be able to pass on accurate information to the new broker. Your new broker may claim they are mandated to use a method to assign an estimated cost basis to such purchases. Fortunately, these should be "non-covered" securities for cost basis reporting on a 1099. They should not report the cost basis to the IRS when these securities are sold. You will not be required to include broker cost basis information on your tax return for non-covered purchases.

Should you change the cost basis/gain realized of a security in your records if the new broker uses different figures than your old broker? Generally, I would say "no". The only reason to change your records is if you find the new figures are more accurate than your records. If you have been keeping good records this will be a rare event. Remember, the IRS holds the taxpayer, not their broker, responsible for the accuracy of tax returns. In fact, I have read IRS regulations that the taxpayer is required to use their own records if they know the broker records are wrong and their own are more accurate. (Sorry I do not remember the reference right now. If you want it, post a reply and I'll search for it.)
A change in broker records for your holdings when a broker merger occurs should be a rare event for a well planned and executed merger. Just-in-case, be prepared.

Russell Malley