Hey TheEquityLab,
Thanks for the detail - it sounds like the payment in the bank has been added, rather than matched to the existing invoice, creating duplications.
The easiest way to remove the payment added from the bank is to go to Banking > Reviewed and select 'undo' against the transaction. You can select multiple here at once and use the 'Batch' function to undo many. This will take the transaction back to the for-review tab, where you can match this to the existing invoice payment (if the payment date and amount matches), or exclude the transaction, as you already have this recorded.
Transfers from PayPal should be marked as transfers on the For-Review tab of the PayPal account and matched to the relevant deposit in the bank account - to rectify this, undo the payment in the bank account, then select this transaction in the For-Review tab and select 'find match' - this should show the existing transfer to match to on the following screen.
Get back to us if this does not fix :)