Ok, since the engineers are busy, there is another to fix it. At least it worked for me. In this case I had the invoice, payment, and deposit as separate transactions. 

I put a line item in the deposit to match the amount of the payment. Deleted the payment from the deposit. 

Then deleted the payment. Then enter the payment again and have it go to undeposited funds, Then go to the deposit you previously altered, add the payment and delete your placeholder line item. This will save the matching and reconciling you have previously done.

I only had one invoice to do. It took a couple minutes and it is a bigger pain than having it be right in the first place. However, if you need it fixed now, this could work for you too.