You are entitled to a refund because your upgrade cleared prior to check-in. Below is from the AC website:

Preferred seat selection charges are non-refundable, except if:

You are not seated in your originally selected Preferred seat because of an involuntary schedule or airport change (e.g. flight disruption, cancellation), or because Air Canada moves you from an emergency exit row seat prior to boarding or during the flight;

You have a confirmed upgrade to Executive Class or Executive First prior to flight check-in;

You cancel your itinerary, or voluntarily change to a different flight or fare family and Preferred seat selection becomes complimentary on your new itinerary.