There's no need to delete the transactions, SarahEC70.
This usually happens when the reconciled checks are not linked to the open bills. Instead, they were recorded as regular checks. To fix this, we can edit the account that is used on those checks to Accounts Payable. This way, the amount will become an available credit to the vendor.
Then, pay the open bills using the available credit (from the article, scroll down to the Credits section. Don't worry, this will not affect the reconciliation as long as the bank account and the amount stays the same.
You can always leave a reply if you need anything else. Thank you.