I wouldn't get too worked up about it. There are many similar examples across the spectrum. Take a look at this link and you will see that under BE02, they list Beech 1900. Any questions could be answered by pointing out that the local CAA has designated the same aircraft with a different moniker.
Part IV - Personnel Licensing and Training - Transport Canada
Assuming that you have also been logging the aircraft registrations, it shouldn't be too hard to validate your times. That said, it wouldn't hurt to get your log book certified with an accompanying letter from the chief pilot stating your total times on the aircraft. If you really want to be sure, contact the folks in Personnel Licensing and ask them what you should do.