Filed 1040X inadvertigly during audit, early in the process, then agreed to IRS audit results and signed and paid 4549. Now what will happen to 1040X?

what will IRS do in this case with 1040X when it finally progresses enough? Will 1040x be rejected due to agreed audit results? Does audit results, especially if it's agreed to,  prevail for the year in question and no new amendements are allowed?