You can change your filing status by filing an amended return using Form 1040X.
If you or your spouse (or both of you) file a separate return, you generally can change to a joint return any time within 3 years from the due date of the separate return or returns. This does not include any extensions. A separate return includes a return filed by you or your spouse claiming married filing separately, single, or head of household filing status.
So the IRS is correct. However, you can argue and debate the fact that if the statute of limitation has been extended for IRS than it should be extended for the taxpayer too and hence, he should also be allowed to amend the tax return and provide it to the IRS. and if as a result IRS thinks that they cannot issue a refund....than you are willing to forgo it.
But they should not impose the hardship of tax liabilities when in fact you are due a refund.
All the best with your contest with IRS. If possible, I would suggest you to involve a tax attorney in this matter.
Let me know if you have any question.
Please note: This advice is provided with the understanding that all the relevant facts have been provided by you. Any change in facts might affect the advice given and hence may not be relied on in such cases. Nothing contained in this reply was intended or written to be used, can be used by any taxpayer, or may be relied upon or used by any taxpayer for the purposes of avoiding penalties that may be imposed on the taxpayer under the Internal Revenue Code of 1986, as amended.