Upvote:4
Yes, this will affect you negatively, because from Canada's perspective it is a refusal. It's a very unfortunate refusal, because most likely you had been approved for the visa and Canada was going to stamp it in your passport.
(If it was possible to do, you should have submitted your passport for visa stamping, even though you could not go on that specific trip. Then you would have had a valid Canada visa you could use later for future journeys.)
You will have to disclose the visa refusal whenever a country asks specifically about visa refusals of other countries. But if the country does not ask, you do not need to disclose it.
The best way to clear this up is to reapply for the visa and be approved. Then, if anyone asks about the refusal, you can simply say you reapplied and got the visa.