One other thing to add, if both spouses did not both file a married filing separately return before submitting the amended return to change the filing status to married filing jointly, then after the adjustment is made, that one original return with its original numbers becomes associated with both spouses on the tax return transcripts afterwards. That could be a problem if return transcripts are needed for income verification.
So, while the original advice here that a second MFS return is not needed before amending to MFJ is correct and true, it may be in your best interest to do so any way, if you want your tax record complete. Also, I suspect the IRS examiner would have preferred this in my case and might not have delayed the return, as original return processing is automated while amended return processing is manual. Doing so probably saves them a lot of work!
