I did just that, just filed the amended return to change filing status from married filing separately to married filing jointly, acknowledged as received on Jan. 15 by IRS.
Now over 16 weeks later, return still has not been processed by IRS. Amazingly, IRS representatives have no way to check up on the amended return further, and they are advising that it might be lost and to send it in again to normal filing address and wait another 16 weeks for a perhaps different result. That's not very definitive, and having the same amend return processed twice might be bad, so I've instead asked for a Congressional inquiry as to the return's disposition before sending the amended return in again.
It's a bit strange in my case, as filing separately would result in a balance due and late filing penalty plus penalty and interest on the amount due, but filing jointly results in a very large refund! So, by skipping the separate filing step, I am also dodging penalties, and I can see how they might not like that! In fact, even if money were owed on the joint return, it's not clear to me if the late filing penalty would apply on the added spouse somehow if the original separate return was filing timely, as amended returns are handled by IRS as a request for an adjustment to a previously filed return and not as a new return.
