I think this is my issue and solution. How do I know what to change the DAYENDNUM to?
From DjangMan: I think this has to do with a day end number assigned to the credit note and when day-end is run it looks for all documents with a number that is higher than the last time. Your credit note is being missed each time. The trick is to reset the right field so that the credit note can be found.
Now that I've described all that, I can't seem to find the table that holds that value. I'm going to guess that it might be BROWSENUM in OEOPT and compare that to a new credit note's OECRDH.DAYENDNUM vs the DAYENDNUM on the document that Sage isn't processing.