Flowey didn’t kill the evacuated monsters
One idea that is seen proposed fairly often is the one claiming that in a genocide route, Flowey kills all of the monsters that we never get our hands on during gameplay such as those evacuated by Alphys.
This is not the case.
First things first, because we know where Flowey is during nearly the entire route : He is following us.
He can be seen stalking us throughout the underground on several occasions :
And in a genocide route in particular, he helps up gaining time in a different way too : He solves puzzles for us as we progress.
Flowey cannot be out there killing the evacuated monsters if he’s with us the whole way through.
In fact, we can know for certain that by the time we are about to leave the CORE, the evacuated monsters are still alive.
If we abort the genocide route by sparing one single monster in the CORE, we can still get the Alphys ending. In which we can see that the evacuated monsters are alive and well, with Alphys now in charge.
The total population of the underground is also far larger than what we see in the game. There are thousands of monsters in total living in places like the city.
The ratings of Mettaton EX’s battle can get as high as 15 559 without cheating.
And we know that those ratings do correspond to the number of viewers.
Between the time where the Alphys ending cannot be gotten anymore and the time Flowey gets scared of Chara, there is less than two minutes of gameplay.
How could Flowey have the time to kill all of the surviving monsters in under two minutes and have the time to go back to New Home ? And that isn’t even counting other problems such as “how could Flowey kill the amalgamates ?”
He just cannot have killed them all. Especially now that he doesn’t have the ability to SAVE anymore either, why would he even risk it now that he can’t bring himself back to life anymore ?
Flowey himself is pretty explicit regarding the fact that there are still people around in the underground to be “freed”, why would he say this if he had killed them all ?
Those monsters are still alive, up until the erasure of the world that is.