Flying a drone around is easy. Identifying who is on the in group and out group and then moving them is the hard part.
I’m not sure you have really thought out what the drone part is meant to do. Militaries gave outgunned populaces for decades at this point. You don’t need drones to kill civilians.
It's actually quite easy. Whoever isn't in the bunker is the outgroup. You only needed to tell people apart when you needed some meatware to man the factories and work the fields.
Militaries can side with the crowd, or more likely decide to keep the power for themselves.