This happens all the time.
There aren't any real ramifications to it. If a customer thought the item wasn't sent, you could reply with the direct link to the Canada Post site and explain that there is a delay in eBay's tracking updates.
If a customer opened an INR case, you likely could easily link a CSR to the Canada Post page if for some reason the tracking was still stuck in the INR case.
It would be nice if they fixed it, but I don't think it has ever caused me any issues in years of selling.