Good morning.  I had this same issue and was able to correct it to reflect the paid amount to the vendor. I made a deposit payment in March, did not receive the bill until July.  

Right Click and select to edit the transaction

Make sure the date of the bill is before the payment.  

In the column, "Account", change to Account Payable

In the column, "Customer Job", make sure the vendor is reflected.  

That is how i did it and it worked and showed a zero balance. 

Hope this helps.