Yes, even if the ticket is changeable, you probably are in for a re-fare. If you booked YSJ-YYZ, and the YHZ stop was originally booked as a mere 'connection', then you more than likely would owe additional fare.
(as this is an example of 'hidden city' ticketing).

If you examine carefully the AC tarrifs applicable to your ticket, AC's only obligation is to get you from YSJ to YYZ. Uncle Milton could even turn up in his private jet, personally pick you up at YSJ, and deliver you to YYZ if the airline wanted to, and they'd still be well within the contractual terms.

Anyways..give them a call, and be prepared to fork extra. On Latitude fare, it looks like approximately $200 w/taxes to re-fare.