Well, the problem is that aplying HQ2X filter without making the resolution higher it would just destroy detail without enhacing them at all. You can try it. Get a background, apply HQ2X, reduce the image to it's original size and compare it to the original image.
Anayway, if you simply want to do it, there is no program yet to reinsert the backgrounds after modiffying them. The format is already mostly decrypted (if it wasn't we wouldn't even be able to display them), but no-one has bothered making a program to reencode BMPs into level files (probably because right now is completly useless).