Can I refund only the commuter pass for the IC commuter pass?

It is possible. The refundable amount of the commuter pass [commuter pass fee-(220 yen * x 2 times <round trip> x number of days elapsed)] will be charged 220 yen and the remaining amount will be refunded. If the balance is less than the commission, the remaining amount will be charged as a commission.
※The amount of the 220 yen portion varies depending on the type of commuter pass you are using.
(Example: 110 yen for school commuter pass (elementary school students and younger, 110 yen section)))
You can continue to use your IC card as a registered IC card without regular use. You can also purchase a commuter pass again when you need it.
From the spring of 2022, the following fees will be charged for PASMO refunds.
(1)If the balance is 0 yen → There is no refund fee.
(2)If the balance is between 1 yen and 220 yen → A full refund fee will be collected.
(3)If the balance is up to 221 yen → We will accept 220 yen as a refund fee.
※The deposit (500 yen) will be returned to the customer in all cases (1) to (3).

※"PASMO" is a registered trademark of Pasmo Corporation.