my thought...
make a box 1 unit tall, 1 unit floating above the floor (make sure it doesn't touch anything)
apply a nodraw texture...
only problem with that, is the portal on the floor will be 2 units above the floor...
OR
make a brush the size and shape of the floor, make it a func_brush
if the stairs are up at the start of the map, disable this new func_brush, if they are down, disable the stairs func_brushes
on door full close (or open, however it is when the stairs are all the way down) disable the stair brushes, enable the new brush
Trigger that moves stairs up, disable new brush, enable stairs.
hopefully that would work, pretty sure you wouldn't see the transition as long as you textured them right