We currently have the same issue. How do we process the invoice?
0 - Create a term of payment with the following configuration

1 - Create and confirm a purchase order. You have to set the terms of payment to the terms we created in Step 0
2 - When you receive the vendor invoice, create an invoice journal for the vendor invoice. Credit will be added to the vendor´s account
3 - You receive the order
4 - You invoice the order - Since it was created using the terms of payment we just created it wont add any credit to the vendor's account.
I hope it helps. If you need any help just ask me