Keep in mind that Gaia's Counter-Force and Alaya's Counter-Force are different things.
The latter probably no longer exists, unless Illya herself is capable of maintaining the collective "will" of humanity.
Also... This is a strange situation. If this were truly meant to be a Lostbelt that was to be pruned, then would Gaia be active? I think yes, since even a pruned world would struggle to exist.