I took that "Paris incident" differently than you did. I felt it meant that, at the moment he woke back up in the helicopter, the omega was now dead in that timeline at that moment. Meaning, none of the stuff with J-Squad happened at all in this timeline. It is fairly evident from them showing similar yet different stuff happening, culminating with him walking into the room where Blunt is training but everyone saluting him because he's a Major this time instead of as a Private. So none of the people died, the beach battle didn't happen, etc. The omega was just dead right that second he woke up, as were all of the other Mimics, and continuity be damned.