To be honest, leaving an account open with a check book being stolen would require a fee type service on the account the makes a signer on the account approve all payments issued from the account before it releases the payment because the account is now considered compromised. It is a service only offered to business accounts at some banks, the service costs money - most business accounts would not choose to do this unless they are larger business. If he contacted his bank and said "my check book was stolen", and he didn't agree to adding this service, they'd place a hold on the account. Simply "cancelling" checks doesn't do anything, that stops those checks. It doesn't stop any counterfeit checks or ACH payments made from the checking account associated with stolen checks.

But - say he said "I simply cant find my checks somewhere in my house and I need a new book issued", IF they were buying checks through the bank, it would automatically start the next book in order (say he already had 001-025, next book would start at 026). Some customer service reps have more access to the ordering system and are able to change the number to whatever the customer requests. You can also order your checks outside of the bank, you are able to enter whatever number you'd like.

All this being said - if his checks were missing, he could either issue a check from a new account, get a check printed with his account information on it for a small fee or just get a cashier's check. Bottom line though, I'm not sure if this is in every state but - paying employees late in my state is pretty illegal.