Ryan
Most likely someplace in between paint can fade and you just loose the shine, not bad. Also paint starts to deteriorate and the bond is bad. You've seen cars with flakes and spots that peel, really bad.
You can take it down to the glass if it is really bad, but most likely you just need to give a good surface for the paint to make a mechanical bond. The solvents in the new paint melt into the old paint. You want a fair surface that is not flaky, chipped, raised, and the paint and glass seem as one. If you scratch at the paint it acts like the fiberglass if that makes sense.
Usually you do the prep work sanding, filling, ect. Then use a wax remover on the boat - wipe on wipe off then prime the boat. At this point you can go over it again and use fine paste filler like everclear to do the fine touchup, sand, wax remover then paint.
The middle step is not necessary it just depends on the quality of the paint job.
I'm a bit anal but my paint jobs usually come out nice.
Have your paint guy look at it he can tell you how far it needs to go.