Amending from married filing separately to married filing jointly?

My husband is in the process of amending his 2007 tax to file from married filing separately to married filing jointly with his ex-wife (they were still married). Now, since they both received refund when they did it in 2007 (filing separately), and he's amending it to get the education credit, will IRS deduct the original refund in 2007 to the amount owed to both of them after filing the 1040X?.