First, acquire some side dots in your choice of material. I prefer to get it in rod form, but you can buy individual dots. Carefully drill out the existing dots and fill with wood of a similar colour. This may not be easy because the dots are usually part on the rosewood and part on the maple. But the most professional way is to fill the old dots to match the surrounding wood. In this case I might even make up a rod that was half its thickness in maple and the other in rosewood. This would definitely be easier using the filler pieces in rod form. I can't imaging the dots holding together very well if they consisted of two pieces.
Glue short pieces of the rod into the holes of the original dots. When dry, cut to length, trim to flush, sand and seal.
Then drill the holes for the new position markers at the desired locations. Glue in the rod as above, cut, sand, seal. If you have scarred the edge of the fingerboard in the process, it not a big deal to float a bit of new finish over the area, smooth and buff. A fussy job, but not all that difficult.