RE: Clearing Extra Payment on an Invoice
I would enter an invoice in AP for the full payment amount. Put lots and lots of notes as to why you're doing this (since it is going to be a fake invoice). Save and post.
Then apply the manual payment to this invoice. Now everything is in history and out of open.
Here's the fun part to get it all right:
Enter a Return transaction in AP for the whole payment amount. On the right side of that screen, use the Cash or Check field and enter in the same payment amount. You'll get prompted to enter a transaction or check number, checkbook ID and a date. Select the correct checkbook where the money was sent back to you and the date field should be the date the payment was returned from your vendor. Save and post.
This will get you back to $0 and show the money coming back to your bank account. This will also get your vendor history balances all correct too (amount paid, etc).
Also, you won't have to do any voids.
I hope this helps. Any questions, let me know.
Thank you.
Joe