How do I unapply and reapply payments bill payments from closed accounting periods?

@DA2018  Reconciliations, and closed periods in general, are dependent on the final results being unchanged. Same amount of income, same amount of deposits into bank accounts, same amounts in each expense or COGS account, et cetera.

Whether you can make these kind of changes without causing problems for the closed periods or reconciliations depends on the details of the wrong bills initially marked paid, the correct bills not marked paid, and whether you are cash or accrual. Since you're using bills, I'd assume you're accrual.

In short, to answer your question, you'll need to provide more specific details about the mistakes.

I doubt it'll affect the reconciliations since those depend only on money flowing in and out, but you don't want to make a mess of information used to, say, file past income tax returns.

Nothing would change with the switch except for what payment was applied to which bill.  The GL accounts would remain the same, as well as the amounts.  The bills are on the same vendor account, but they all got reconciled prior to the current accounting period.

@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.     

@BigRedConsulting 

Great tip!  I mistakenly assumed the vendor needed to be changed (even though the OP stated it was the same vendor - oops).

I'll add that it shouldn't be necessary to go back and unapply/reapply the payments.  If the payments were reconciled on the bank statement and the bills were entered for the correct amount, then there should be offsetting A/P debits and credits that can be applied to offset in the current period (this is double-entry accounting after all).