What does it mean to reconcile checks?

Either pay it or come to an agreement with the company. If you are reconciling a cash account, it means to identify all of the differences between your balance and the bank's balance. Your checkbook might show $100 balance but the bank says you have $109. Why? Because you wrote a $10 check that has not been cashed, and the bank charged you a $1 fee that you didn't know about. So you subtract the fee, bringing your checkbook balance to $99, and when that outstanding check hits the bank, they will also show $99. If you are reconciling some other account, like accounts receivable, this is normally done by preparing a detail schedule, a listing of all customers and their balances - the total should agree with the total ledger balance.