Flies are small... you'd need a lot of light, multiple angles and good cameras/lenses to decently illuminate the flies, which has the problem that all the light will only attract more flies.
That camera system tracks a single, largish object in perfect lighting.
I think the biggest problem with insect tracking is focus: They are so small that they can only be recognized if they are perfectly in focus, so you probably can't track them in 3D volumes.
Maybe you could track them with clever lighting tricks. Eg. illuminate room with very bright light coming from the side, with a black wall, so that mosquitos show up as bright spots in the video.
I think it would be fine if you tracked only the flies that entered or exited through the small hole in the wall, ie not tracking the whole room just a tiny corridor.
So yes, you know the delta-fly(er) but not the number of flies.
And if there were a small door over the hole, that opened only to allow fast moving flies to go through it from one direction and slow moving flies to go through it in the other...
Surely we cameras good enough for fly tracking technology in 2021?
[0] https://en.wikipedia.org/wiki/Hawk-Eye