Quote from Burnf
We have the elders of Mirrodin, infected with mycosynth, were all sent home to their native planes back in Fifth Dawn.
It's been a while since I read Fifth Dawn, but if I recall correctly, the people brought to Mirrodin by Memnarch's soul traps were returned home as if they had never been to Mirrodin; no memories and no metal enhancements. No metal enhancements means no mycosynth.
There are other Phyrexian factions out there, because of Karn's traipsing about the multiverse dripping oil everywhere he went, but that continuation of the Great Work was completely independent of the Vanishing.