Some of it will depend on the expectations of the customer and the condition of the fretboard.
Recently, I replaced the frets on a well-used Telecaster. The customer didn't want the fretboard cleaned-up, which was an advantage in some ways. I eventually cleaned-up the areas of the fretboard that were under the frets. I explained to the client that doing this would help the frets seat better.
Since the client didn't want the fretboard re-lacquered and, in fact, didn't object to more relicing, I didn't protect the fretboard during leveling the frets.
This is a photo after the frets were removed. Most likely the areas around the frets had been cleaned-up a little at this time, too.
Even before removing the frets, some of the lacquer had come off. This was fine with the client.
I heated each fret before removing it to reduce chips.