Hi SSchultz
Typically when a reconciled transaction was edited or deleted & re-entered, it will become an unreconciled transaction. If you didn't edit the original pay, only reversed & re-entered it, then the reversal and the re-entered pay are unreconciled transactions, you can tick and reconcile them in the same period.
As of the payroll clearing account, please click into the payroll transaction(s) showing, hit Ctrl + R to recap the transaction, is it crediting the payroll clearing account for the net pay amount? If so, check the payment method used in the pay, then go to Setup > Linked Accounts > Payroll, the linked account selected for that payment method is where it would pay out from.
If you have any further questions please feel free to let us know.