Booking an AC codeshare is irrelevant, because bonus points are always based on operating carrier. AC confirmation showing an EN flight number doesn't mean that was EN operating as EN, because AC doesn't always handle codeshares well. Another good reason to avoid codeshares.

For future reference, the best way to establish this in advance is to consult other resources, whether the LH website, EF, Google Flights, etc and look at the flight in question as a non-stop. That should tell you whether it's EN operating as EN or EN operating as a regional on behalf of LH.

(Yes, this whole system is stupid and terrible, and I'm not defending it. But it's still not clear whether you were actually entitled to bonus points here)