Welcome to the forum! A very good question indeed.
I actually ran into this situation once. After receiving permission from the stake leaders, the deposit bag was sealed (without the slips) and the Bishop kept it with him until Monday morning, where he took one of his counselors with him to the bank and made the deposit in person. He used a generic deposit slip from the bank office and they didn't leave until the bags were opened and the funds verified against the MLS printout. A copy of the deposit slip was then given to the finance clerk for the files.
Not a good situation to put yourself in.

While at the bank, the Bishop picked up a few more generic slips to have just in case the slips on order didn't arrive in time for the following Sunday's batch.
For lack of a written procedure, this was the best we could come up with on the fly. Thinking back, I'm not sure of anything we could have done differently to protect the integrity of all involved.
Good luck,
Mike