I asked a similar question more than a year ago. Advice given was excellent and has worked well with no issues. Use my Canadian passport with AC. Use my EU passport (at passport control) to exit/enter EU countries.

After Canada started requing entry visas I had huge difficulty checking in with AC, despite having contacted them to change the passport info for return flight from EU to Canada. Online check-in couldn’t be done. At the airport a very capable AC agent also had trouble and it took close to an hour to fix.

I have never been flagged on arrival in the EU (��) and used the electronic gates several times as well as gates with an actual person. Just remember which passport to use and put the other one away.