Hi. Hopefully you have found a solution since already.  I too had the same problem with my AP Aging Report.  The report listed all the old transactions even though the customer had no balance.  This is how I cleared them up:

1. Go to the Pay Bills Screen

2. Filter for the vendor

3. Select a bill

4. Select the Set Credits Button 

5. From the Discounts and Credits Screen, find the corresponding JE, select it

6. Select Pay Selected Bills

7. Run your AP Aging Report to verify the off setting transactions no longer show.ope that 

Hope that works for you.