Forget the "fees may apply" language. This is boilerplate generic disclaimer.

Check the specific fare rules for each direction of your ticket. Under "Changes" or "Cancellation" it will either list a fee, or it will say "Cancellations Permitted." By saying that, it means it is refundable. Note that the most restrictive fare rules apply to your entire ticket, which is why you need to check the rules for each fare component/direction of your ticket.

As for seat selection and upgrade fees, these are generally nonrefundable even if you cancel/refund the ticket as a result of a voluntary change. If there is a qualifying involuntary change that would allow for a refund, then your seat selection/upgrade fees, even if initially disclosed as nonrefundable, can be refunded due to the involuntary change.