Well, the Invae always have their home plane to fall back to, or where more of them might lurk, so they might be safe from the Horrors there.
They might also have held out in Barsaive (or some other part of the world) in underground cults and in hiding. They were living among people before, using them, and this might well have happened in the kaers too.
The queens are usually the last ones to enter the physical world, so at least in Barsaive, where the Invae were fought off, they wouldn't have had that capability. Except if you still have some very large, unopened kaer where the Invae managed to gain the upper hand during the centuries of the scourge. A giant kaer the size of a large city ruled by an Invae queen would be interesting, with many of the population being taken over by Invae spirits on a regular basis.