I have had a few customers try this on me too. When I think a customer may do this to me, I get a few of the boxes with lots of wires in it and "accidentally" not connect a couple of wires....I just cap them off and hide them behind the other wires. I also mark these down on my note pad and when I come back to do the finished wiring, I correct these "mistakes". If they choose to do it themselves, they will have a fun time troubleshooting.
I've also used the # method that Bossman stated above, and have a cross-reference on my own note pad.
My contract states that any warranties for my work become void if anyone else other than me or my employees finish the work. This usually keeps the customer from considering doing their own work.
