This is an atrocity that must not be condoned. When you lose the tone holes, the sax is pretty much done. Minor restoration can be done by pulling the tone hole up using dent tools but this is not really the ideal situation either. Excessive filing/sanding on tone holes is probably the worst thing that a tech can do to a sax because it really can't be 'undone' like most other things they do to them.
BTW, you can't file on Martin soldered-in tone rings either, because they are tapered. As you file, the rim gets wider and wider. These tone rings are quite thick compared to the body tube and they most likely are not going to warp and should never need anything but a non-abrasive cleaning. Martin made replacements in case of severe damage but of course they haven't been available in decades, so anyone working on one should forget about filing the tone rings.
Going back to the drawn tone holes, 'pulling' is used to correct 'dishing' that used to be frequently seen after a bad buffing. When you are faced with a tone hole that has been filed down excessively for reasons unknown, it might not be possible to pull it up enough to restore the horn.
I am of the opinion that there is way too much emphasis placed on leveling tone holes and the whole thing is way out of hand. A very light 'clean-up' is one thing but even that must be written down and provided back to the customer so there is a record of how many times this has been done - and it shouldn't be done more than once or twice in the life of a sax. Now, when there is damage that affects a tone hole, some leveling may need to be done - everybody understands that. But the techs must understand that the new sax came from the factory with finished tone holes with no extra material for later filing. Every time brass is removed, the tone hole gets shorter and is no longer as it was from the factory. This means it is now wrong, and it can never be original again.