Hi Amber
First, make a backup under File | Backup | Accounts Payable data, just in case.
Then you should reverse all of the checks that you want to reprint, and post the check reconciliation. The invoices you need to reprint will now be outstanding.
It's hard to follow the flow of what happened, but it doesn't really matter because the bottom line is that you need to reprint the checks, but Adagio thinks the checks have already been printed and are posted to the vendors' accounts.
Steve