Discovered IRS made error on Form 4549

What if this is discovered after the audit adjustments are agreed to? In this case the indivual return was only examined to account for an S corp audit adjustment that was agreed to, but the effect on the individual return was not adjusted correctly by the IRS due to basis limitation issues. Can the return be amended to correct the IRS error and if so are their special procedures to follow? Thanks.

I don't believe it can be amended but as long as the tax is unpaid you can get IRS to correct the 4549 form . I recommend you review Pub 3598 " What you should know about the audit reconsideration process" . Also you would probably want to explain your findings on form 12661.