Hi!
The old Biter Expansion feature wrote into your map settings: it switched expansion on, shortened the cooldown, and made settler groups larger. Those values stay in the save after you delete the mod, because no mod code runs any more to put them back. More nests means more units, so the units come back after you kill them.
Research Pressure also spawned extra biters that carry vanilla names, so they survive the uninstall too.
I removed the expansion feature in 10.9.4 for exactly this reason.
Check your map first (read-only):
/c local e=game.map_settings.enemy_expansion game.print(serpent.line{enabled=e.enabled,min_cd=e.min_expansion_cooldown,max_cd=e.max_expansion_cooldown,min_grp=e.settler_group_min_size,max_grp=e.settler_group_max_size,dist=e.max_expansion_distance})
Vanilla is min_cd=14400, max_cd=216000, min_grp=5, max_grp=20, dist=7. If your numbers differ, copy your save, then run:
/c local e=game.map_settings.enemy_expansion e.min_expansion_cooldown=14400 e.max_expansion_cooldown=216000 e.settler_group_min_size=5 e.settler_group_max_size=20 e.max_expansion_distance=7 game.forces.enemy.kill_all_units()
Set e.enabled=false as well if your map started with expansion off.