[quote]and you only have 3 years to amend a return...for 2009 that would have been as of April 2012.
Uh, no. There is a three year statute of limitations to claim an OVERPAYMENT from an amended return. You can actually amend a return whenever you want, though there is little point to amending it after the statute expires IF you are due an overpayment. That doesn't seem like the OP's situation.
And let's take out our fingers and count again. The statute runs from the DUE DATE of the return. The 2009 return was due 4/15/2010 ... so three years after that was 4/15/2013. The OP said he sent in the amended return "three months ago" so that would easily be before the deadline.
That said, the OP's story does sound rather vague and incomplete (e.g., did the original return show you owed money, and did you pay it with the return?), and I really doubt he actually told the IRS "I don't owe you shit." :)
However, as I have said before, the IRS is having an EXCEPTIONALLY BAD YEAR (and this is unrelated to the current "tea party" flap, which has been somewhat exaggerated). and I've seen some extremely weird notices they sent out, so anything is possible.
I just took care of one notice where they insisted my client never filed her 2012 tax return, and the notice referenced the Document Submission Number, which is issued by the IRS only when they DO receive an e-filed return,
Another received a notice that he could ignore a previous notice which was sent out erroneously. The problem is that the taxpayer never got a previous notice. He came over and we called the IRS. They said that the previous notice may have been "delayed" a couple of more weeks and could be ignored when it arrived. Uh, follow that? It's like them saying "I'm GOING to make a mistake and mail you a scary notice that is wrong, probably in a week or two." Why not just NOT send the wrong notice?
Bottom line: Don't be intimidated by an IRS notice and assume they are right ... ESPECIALLY THIS YEAR. If it doesn't make sense, make them explain it to you. Don't just send a check.