Total failure for QB.  But I found a round about solution until they fix it. 

1.  Go to the original invoice.

2.  click "Create a Copy" (but make a note of the invoice # of the original!) this will bring you from the original to the new invoice and will have a new invoice #.

3.  Click "Save & New".

4.  Bring up the original invoice and delete it.  It will tell you that it will leave a credit of the original partial payment on the customer's account.

5.  Bring up the new invoice that you had created. 

6.  Change the invoice number to the number from the original invoice.

7.  Click on "Apply Credits". (the remainder of this step is self-explanatory)

8.  Email the new invoice to your customer.  They are now able to pay the remaining balance online.

I know this is a pain but at least it is a solution... and hopefully VERY temporary!