They are basically telling you that they got the amendment and are processing it, and will get back to you when they are done.
Do NOT lose any sleep over this. They got the amendment, and they cashed the check. The rest is a paperwork drill, with MAYBE a small interest or penalty that will be billed to you sometime in late August/early September. Given what they ORIGINALLY asked for, I suspect you will gladly pay that bill if and when you get it.