Refund services actually replied to my email today. However, all they said was they have forwarded my request to the ticket copy and usage department. I will give them a couple more days.
In the mean time, we also sent copies of everything to Royal Bank, which is the issuer of the VISA card.
My sister has all the paperwork now; I asked her for more detail, and everything she told me was just odd.
She said as soon as my dad saw the extra charge, she contacted Royal Bank to dispute the charge. In April, Royal bank sent us a letter saying Air Canada could not come up with a charge slip, so they took that charge off of the VISA account. We thought the matter was settled. However, a few days ago, we received another letter, stating that they have completed the inquiry. Air Canada provided the charge slip (copy enclosed), and they will put the charge back on the account.
The odd part is that the charge slip was very blurry. It showed something resembling my dad's credit card imprint and signature. However, it does not show the date of the charge, nor did it have any information other than a ticket number. It also shows the total as more than $10,000. (That would definitely get our attention.) The ticket number was not the same ticket number as the ticket my dad used to travel in December. Since my dad was SE, he certainly has a lot of old tickets. We haven't been able to get to my dad's old tickets to verify if the slip was from any of the other tickets that he had paid for. Finally, the amount VISA put back on his account was not the same amount shown on the charge slip.
Right now I wish my dad had used an AMEX card. The same thing happened to me last year, and AMEX took care of it before I even noticed the double charge. (The ticket number was different as well) I'll keep you all posted on the latest developments. Thanks for all the suggestions.