Just an update: After hours of googling, I finally found a number that one could dial from outside Canada. After being on hold for at least 30 min I got through to a v nice agent at the CIC who assured me it would be fine but to bring the old passport just in case.
Now, the even funnier thing was that when I woke up the morning after, the same day as my departure, I had an email from them that the eTA had been approved! Had it not been so stressful the previous day I would have found it hilarious...