To adjust transactions that have been reconciled, first pull a copy of your reconciliation report. To do this, go to the Accounts tab, right-clicking on the account name and select Notes & History from the menu. Once in the notes, follow the link to download the report.
To un-reconcile transactions, head to the accounts tab, click on the balance, scroll to find your transactions (which will be marked with a bold "R" in the far right column) and edit each transaction in question using the pencil/paper icon
and adjust the transaction from "reconciled" to "uncleared" and save your changes.
We recommend you add in a new note to the accounts "Notes & History" to ensure you have a clear trail of the chain of events. Once you have un-reconciled the transaction, it will be available for a new reconciliation.