Glad you asked this, I have the exact same situation with a $150 refund From a voluntary schedule change last fall. The agent gave me the certificate number over the phone, I wrote it down somewhere, and I haven't seen it since. Sounds like the best bet is to start with the ticket number from the changed itinerary and try the website first, then the phone if necessary?

Somewhat tangential question, if I'm booking an itinerary for 3 pax and would like to apply both this cert and a 10% off cert from an IROPs situation can I make the reservation under a single PNR, of doe it have to be split to apply both certificates?