The lettering kept the gelcoat under it from oxidizing. Unfortunatly the newly exposed gelcoat will not oxidize any faster than the gelcoat that has been exposed for decades.
You could hand wetsand with a board the full size of a sheet of sandpaper the newly exposed gelcoat down so it is level with the rest of the gelcoat. You could also rent a long board which is a powered sanding
board with a long strip of sandpaper. It is used to get hulls super fair.
Or you could not worry about it and put new vinyl letters over the partially sanded down raised area. I don't think it would be that noticeable unless you are looking for it.
You could also not sand but build up the area around the letters with a sandable epoxy
filler, fair it out and then have it sprayed with an LPU paint
My own inclination would be to sand it flat and then have the transom sprayed which would put an end to the gelcoat oxidation.