Ok well since the nut slots are angled back from the very edge of the fretboard face to the back of the nut on the tuner side then if they are indeed filing the front face notch down then your action at the nut would go down too as that point of contact moves back down the ramp so to speak.
The zero fret option might work out better for you. If you don't do that then you might consider having a luthier make two nuts for you and don't glue them in so that when you are out on a cruise and it happens you can swap it out.
Like I said I've never seen anything like that, there's always something new and interesting that comes up. But I am still wondering if something else is going on, just can't think of it. If I had the guitar in my shop then I would look very closely at the nut slots with a 10x lens and I would be able to see what is truly going on. If you have such a thing you might have a look. Maybe even a close up pic that you could blow up on your computer screen may reveal something too.
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