@DA2018
Unapplying a bill payment requires deleting it or voiding it and applying it to the correct bill requires re-creating a new bill payment for the same date and correct vendor and paying the now unpaid bill. That process will cause issues with the reconciliations. After re-creating the bill payments and applying them to the correct bills, you can clear the bill payments in your chart of accounts in the checkmark column. Find the bill payments, then click the box in the checkmark column until the checkmark appears. That should correct the reconciliations.
There is a trick to do this:
To break the link between the bill and the bill payment without editing the bill payment (and so not impacting reconciliations), edit the bill and change the name on the bill to another name, but don't change anything else. Then save and reopen the bill and change the name back to the original.
Once you've done this for all the bills that have payments misapplied to them, then use the pay bills feature to apply the open bill payments, which will appear as available credits, to the correct bills.
When you apply credits to bills and the new "amount to pay" is 0.00, then no new bill payments are created when you click Pay Selected Bills.