A user accidentally credit a duplicate bill credit and they caught it a little later and created a JE to reverse it out. Now it is sitting on there AP Aging and they were asking me about it. The one solution I had was to "Pay Bills" and select the JE and Bill credit. In sandbox it appears to work and didn't create an actual bill payment (They net to $0). Is there any issue in doing it this way that I am not seeing?

your way is correct - a $0 bill payment is the way to go

Great thanks