The best way to handle this would be to use the following process:
1. Create a Credit Memo (negative invoice) for the same amount as the un-paid portion of the invoice (Please ensure that at minimum the transaction is dated today or earlier).
2. Go to Check Writer and complete a Check on Demand selecting the outstanding invoice and the credit memo, the system will issue a zero dollar check that you can then discard.
If you have any trouble completing the process above, please feel free to open a case with out support team and we will help by walking you through the process.
M3 Support Manager