Not in all scenes. Some scenes are actually cropped and resized, and it’s they’re clearly recognizable.
It’s a hazard that comes with doing this kind of work on older shows. Most of the negative is there but there are always those troublesome shots every once in a while that go missing. Star Trek: The Next Generation had the same issue. In those situations you just have to make do with what you have. The X-Files has the added complication of using old stock footage. I think the restoration house that handled this did quite the commendable job. The only real issue I have are the fonts but the new ones they used are quite pleasing to the eye and pretty close approximations.