Same issue for me but I already have Invoices created.

Steps

1)A bulk bank deposit arrives into my bank feed from my credit card merchant, I save it as a sale of product income split for each client,

2) then go to my chart of account and edit the deposit to A/R.

3)I then go to Receive payment allocate the payments to each outstanding invoice and save.

All invoices not show paid. But the issue is that my bank balance is now way off and now I have a series of "overdue" deposits.

How do I clear an overdue deposit when the invoices are already showing as "paid"?

Help!