Which MFS return did you amend? Yours or hers? You only need to amend one of them to Joint. Then on the amended return you should have entered both spouse's refunds or tax due. 1040X Line 18 should be yjr original refund amount and line 21 should be your additional refund. If you paid on your original return it will be on line 16. If there is an amount owed with the amendment, it will be on line 20.
And if the IRS letter said adjusting the total tax withheld that sounds like something else is going on.
