Hi FW2016,
Thanks for posting your concern in the forum.
I'm sorry to hear about your bank feeds not being matched to the transactions in the system. In my understanding, if the transactions are still sitting in the Prepare Bank Deposit window, you can create a transaction from there to move the amount from the undeposited funds to the bank account of your choice.
I would suggest creating a transaction from the Prepare Bank Deposits window if the transactions haven't been automatically recorded yet. After which you can match this recently created bank transaction with the bank feed.
Let us know if you require any further assistance with this.
Thanks,
Genreve