I am confused about auto-generated sales receipts and how to handle

I used QB Online in conjunction with Acculynx (our CRM). Our typical process is to create an invoice in Acculynx and Acculynx records it in QB. The issue I am having is, any customer that pays via QB payment link, it's generating the sales receipt which is acting as an invoice (of sorts) when there is already an invoice (from Acculynx, see attached). It's throwing off our P/L and there are hundreds of customers we will need to go in and fix.

I thought we could go in to each customer and delete the auto-generated sales receipt but it's giving me an error that says, "This transaction has been deposited. If you want to change or delete it, you must edit the deposit it appears on and remove it first." Do I just need to delete the invoice that was transmitted from Acculynx?

I am also wondering how this works if I stop having invoices recorded from Acculynx, what happens when a customer makes one payment through QB payment link and another with a check? I will need to make an invoice in QB for the difference? It's very confusing.