I disagree with Overnight. I believe it would not be at all prudent to go along with an incorrect 1099-B. I think it would be prudent, #1, to make certain that the 1099 is incorrect, and then, #2, to demand that the broker correct its bad 1099. My purpose, in this thread, is to achieve #1.
I do, however, agree with Overnight that it would not be prudent to file a return conflicting with the broker's 1099. We differ in that his approach is to adjust his return to match the broker's bad 1099, while my approach is that the broker should correct its bad 1099, so that a correct return will match it and avoid IRS trouble.
I also disagree with Overnight's view that it will all flesh out in the end, when the open position is eventually closed. I believe his approach can result, for example, in a very large tax overpayment in one year, and a very large tax underpayment in another year. I think that IRS could find this totally unacceptable, and inflict real pain, rather than sit back, relax, and say, it is OK, dude, it'll all balance out in the long run.