Hi vpfsw,
I was exactly in the same situation as you.
My credit card was also used fraudulently and the card company stopped my card at around May 28th.
I asked my consultant in Canada for advice, and she called the CIC call center (1-888-242 2100). Their advice was to send an email with the new payment form with a new card number. But it was within the six weeks since my application reached to the CIC office, and my information has not registered to their database yet. So, they said they were not sure if this would work properly because it may be difficult to update my card information in the database. My consultant sent an email with new payment form, and also sent the same form via Fax. (however, the Fax No is not opened to public. It seems to be shared just within the consultants..)
However, we still don't expect my card information has been updated properly. So, in the meantime, i negotiated with my card company to reactivate my card. Fortunately, as it is clear the FSW fee will be charged from Canada, card company finally accepted to open the transactions only from Canada. Furthermore, they will compensate in case of any fraudulent transactions(it's important!!)
If you tell your card company about the country and name("Citizenship and Immigration Canada" or just "CIC") of the necessary transaction, i think they may be able to consider of any remedies. Because fraudulent use was not your fault!
I hope me experience will be of some help....