When paying with a credit card what I always do is to enter an invoice for the vendor in PO Receipt of Invoice and then do an Invoice Transfer in AP from the Vendor to the Credit Card company. If they don't send me an invoice I just use the PO number as invoice number, however you should always get a receipt for a credit card charge.

What BigLouie said, exactly.

To clean up the history perhaps do zero $ ROI's for everything you know was paid by CC, then GL fixes posted separately (because the ROI DTR's should post to the purchasing variance account, which is not likely how the CC payment was processed).

On day two of cleaning the PC report, I tried doing a ROI for a PO that had qty ord 200 -qty rec 188- qty inv 200 and on the ROI I invoiced a -12 with a $0 amount.   I am not familiar with the GL/ACCT back end, would this cause any issues?  I am thinking I could fix everything in the ROI instead of having to do a ROG and then worry about inventory.  All these old po's we do not owe anything to our vendor's and nothing needs to be taken out or put in inventory.