I had the same in the first week of July, but by the end of August the EU/non-EU were being split again. The reason I think was that in August now the egates also scan the EU health certificate QR codes, while in July all COVID checks were being done manual and they had to put the egates out of commission.
If you come in without a QR code but e.g., a CDC card on a EU passport then you get pulled out of the line just before the gates and sent to one of the 2-3 EU manned booths. EU took half the time vs non EU (based on what the wait time screens were saying)

FWIW, the current plan is to buy RT JFK-CDG in business and buy separate train tickets to get from ZYR to CDG on the return, leaving about 2hrs30mins for the train to plane connection from 11:53 train arrival to 13:20 plane departure. AF is effectively charging over $1,500 for each train ticket, which is a bit much. We hope 2.5 hours is enough time and if it's too much we can wait in the lounge. This means we'd have to check in at CDG. It sounds as if passport control and security vary from a short wait to a much longer wait. Flights are mid-October.

That's great news! Thanks for the update!