It's certainly been done by people on here before.

They've normally drilled out and filled the old dots. The pro way would be to get a matching piece of rosewood, and using a plug cutter, make some rosewood dots that you glue into the old holes, ensuring the grain pattern is in the same direction as the board.

I'd probably get some wood filler, colour it to match (I use a very cheap set of artists acrylic paint in tubes for this and mix the paint in with the filler) and sand it back once dried. or you could just try a dab of matching paint over the dot,

Whatever finish you plan to use for the back of the neck, you normally also cover the sides of the board with it (masking off the top of the fretboard itself). This will also help protect any filled or painted dots.

Realparts do various side dot inlays, or you can search fro them on eBay or Amazon.