I had a similar issue and found a workaround. However, it may require that the period you are trying to correct is still open. If you have any bill with the vendor, you can try this:

1) unapply a payment applied to the bill. you should now have an open balance on the bill

2) go to the bill, and select "make payment"

3) rather than pick the payment to apply the bill, you should see the debit and credit entries as options. select the offsetting debit and credit entries and make a payment. Effectively you will be applying the debit to the credit. Since it should have net zero impact, your bill should remain open for the amount of the payment you unapplied in step 1

4) go back to the bill, and reapply the payment you unapplied in step 1. if done correctly you will no longer see the journal entries as options

Net impact from these steps should be zero, but you will now see the offsetting journal entries fall off the AP aging report