Get a copy of the ETR.
Show up at the airport a little early on the day of the flight.
In most cases, control of the ETK coupon will be pushed to the Emirates DCS with no issues (this is an independent process to the PNR sync process so should not be affected even if a failure occurred there as it appears it did).
Emirates sees your PNR record for the flights in question. To check you in, they have to associate the PNR record (which is pushed to DCS via the PNL/ADL) with an ETK coupon. If the coupon control has not been pushed, they can request control from the issuing carrier (AC) in this case. It is a simple command and shouldn't take more than 5 seconds. It may however require a supervisor code to make it work. It becomes a lot simpler if you have the ETR record from Air Canada.
Nothing to worry about. Your ticket is issued and you will be able to fly. Only issue is that OLCI and ASR may not be available.