Yes. You can write off credit balances on transactions or customer balances using the Maintenance | Create Write Off Batch function. If you have Adagio Payables, this function can create a Manual Check batch to print a Check for the customer.
You can read about the process in the Receivables Manual (starting at page 5-209) or in the F1-Help or in this Tech Tip from Arx Systems. This "Show me how..." video from our Technical Tips page describes the process: