I’d look at the person making up the bank deposit. They would be the last person to lay eyes on the cash/cheque mix. Cash donors likely don’t want a receipt while cheque donors might, or instead they have their paid cheques returned. The perp stashes the cheques uncashed. Then next day or weeks, packages up the next bank deposits, takes out the cash, substitutes a bunch of cheques brought out from the stash and makes the deposit. So the ongoing tithe revenue looks normal, but the stolen cheques are laundered right in front of everyone over a few weeks. It would take an on-the-ball donor to wonder about the delay in the cheque negotiating, but it might be the same staffer who answers the query and could cover their tracks. The timing difference throws everyone off by focusing attention on the initial theft when instead the real fraud occurred after the fact. So those booklets where you record your deposit and the bank stamps it to make it official? The tellers just wallop it without looking at them. So they show the proper cash/cheque mix but the actual deposit is mostly cheques.
Just so you know, this wasn’t me. I’m neither smart nor ballsy enough to pull this off.