In QB the money received need to be received against the invoice in receive payments, then deposited. Then you download banking and match.

If the CPA will not open the records, the only option is to create a service type item that is linked to the retained earnings account. Use that item on a customer credit memo and apply the memo to an open invoice.

The software is not true accounting software IMO. So you have to use the forms and work flow that QB dictates for things to work properly. Journal entries should be avoided as they are not part of the work flow and do not show in some reports, as well as often not working as you think they should.