Manager has no explicit exchange function. You would normally process a return and a separate sale. For the refund, see this Guide: Pay a refund | Manager.
However, there is a way to streamline the process. Use a Spend money transaction, either in a bank or cash account depending on how the money is changing hands. Enter the inventory item being returned. Then add a line for the replacement item, but enter the quantity as a negative number. This will turn the amount for that line negative. Because the overall transaction is a payment, a negative payment is a receipt. So in one form, you will have entered the return of the item coming back into inventory, just as though you were purchasing from a supplier, and the sale of another. The Total on the payment will indicate how much you owe the customer. In the example below, the customer has returned the white ceramic lamp and obtained the ceramic lamp base instead. Since the lamp base is less than the entire lamp, the customer is owed the difference:
If the exchange were the other way, the customer would owe you:
In fact, if you knew in advance the difference would come out this way, you could use a Receive money transaction. In that case, the item coming back would be entered with a negative quantity. And a positive total would show that the customer owed you. It would probably be good practice to standardize how you enter exchanges to avoid confusion. Always use the same type of transaction, always enter the returned item with the same sign, and you will always be able to interpret the total the same way.