Usually the IRS is pretty firm with this type of deadline, which is 3 years from the due date of the return. Since you filed an extension, the 4 or 6 months extension normally would then be the due date of the return (August or October 15). The problem is the IRS not having record of the extension. I suggest you re-visit the filing of the extension with the accountant you used, and if he is a recognized tax preparer with the IRS, he should be able to prepare a support letter for you documenting the filing of an extension. Hopefully you will be able to then "appeal" the IRS original rejection with this support, the accountants assistance, and the extenuating circumstances of the natural disasters that prevented your timely filings. Good Luck.