Thanks to everyone here, and special thanks to plankton for his sacrifice of EK F and making the forum aware of the problems. Aeroplan fixed my booking and i now have Fare Basis starting in Z.
To recap i made a test booking of home-yyz-dxb and the fare basis for the EK flight came up as ZBP00AFF/AE4. I called aeroplan and after an hour waiting for callback i explained the issue to the agent which surprisingly only took a couple minutes and then she connected to ticketing which was a total hold of 1h15m for her to get back to me (im not complaining). Ticketing reissued and i can confirm on cowtool fare basis ZBP00AFF/AE4.
Im not sure if i showed up to the airport what would happen... my guess is AC would print me EK boarding passes on their stock, i would head to the gate 45m before departure and be met with a grumpy gate agent telling me they cant board me and i would have to rebook with Aeroplan.. Or its also possible my ticket was ok all along but best to not take the chance