Invoices and their System Generated Credits - AP150 Clean-up

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Has anyone bumped into a method that handles the following situation as we would love to have our cash requirements file clean from all of the issues we bumped into during the first year after Go Live?

We have invoices that were reverse matched where the system generated the credit. These could be related to invoices hitting the wrong Process Level due to the PO having the wrong Process Level or the invoice hitting another vendor (in the beginning, we didn't know how to resolve this). Needless to say, our cash requirements has a lot of vendors with zero balances due to the issues listed above.

Has anyone found a way other than forcing these items onto a payment with the correct pay vendor (for when we had no idea how to change this) or allowing zero dollar payments (would prefer not to allow zero dollar payments) that would clean up the AP150?