So I had this fixed on my bass, and so far I'm very, very happy with the results.
One of the folks I play music with is a luthier, and he told me that this is not an uncommon problem with bolt on necks. Granted, it only happens to a very small percentage, but enough of a percentage that it's a known condition.
He ended up removing the last 5, 6 or 7 frets, shaved the fret board down so now it's in perfect line with the rest of the fret board, and then replaced the removed frets with new ones, and did a basic level job.
Okay, he's a person I know and play music with, so the price he gave me was probably way below market. If the instrument is not particularly special (meaning expensive or vintage) you might be better served getting a replacement neck.
In my case this was my main player, a Fender American 62 RI Jazz that's got some age and mojo to it. For me it was without doubt worth the price paid.
Anyhow... that's how this problem got fixed for me, and from what I've found out, shaving down the fret board should really be a part of the solution for a permanent fix, not just filing down some frets.