When do we have to give the money for the deposit to customer A?
when a deposit is made...and since you have no proof of deposit, no deposit has been made. you owe the customer nothing. you certainly are within your rights to let them know you have reviewed camera footage and show a withdrawl fro the ATM, but no night drop box activity.
Then suggest they contact the maker and ask for a re-issue. Although it sounds to me like B cashed the check, possibly at the bank the item was drawn on.