If a bank transaction has been deleted within a statement but not ignored on the Bank Feeds screen, it will continue to populate from the feed through to statements. This causes it to reappear within the Bank Reconciliation.
To prevent this, the transaction must be deleted in the statement as well as ignored from the bank feeds screen. Once ignored, the system will no longer pull it through from the bank feed, and it will stop reappearing in reconciliations.
To do this please delete the transaction on your statement, and then navigate to the bank feeds screen and locate the transaction. 
This should be greyed out instead of green as it is no longer associated to any statements. Highlight the transaction and you will then see a button appear 'ignore from statement' once this has been done the transaction will no longer appear on your reconciliation.
If you accidently delete a statement item and/or ignore one from the bank feed, you can navigate back to the same screen and instead click include in statements to make the item available again. It will then repopulate in your bank statement and reconciliation the next time the scheduler runs or if you click the 'populate bank statement(s)' button at the top of the bank feed screen.