I know the sound you speak of. If it happens at all(some drives don't) it would be during the load up on a RPG game of some sort. The lens moves very far back and forth when loading up the beginning cinema scenes. The sound is the lens hoping around on the track just for a few moments from moving too fast to the stopping point. It is not the gears grinding and shouldn't cause any future issues from what I can tell. The reason there was originally a 3rd gear in there was to slow the speed down. Unfortunately no one has yet to find an exact gear replacement so until then this is the best we have. Maybe someone knows a way to reduce the voltage to the motor to give it less juice?
Also, 50% of the time you can tighten up the tension on the plastic piece that holes the lens to the track and it will fix the too fast skip issue. However it doesn't always work if the lens motor is too strong. Here is a picture of the part I am speaking of and how I bent it down ever so slightly. Do not bend it too much or you could break it and the only way I know of to get another one is to buy a doner CD drive. A very small bend can take care of the issue.
To conclude, if you only here the loud skip once or twice when playing a game I would just leave it alone. I don't see it wearing out parts anytime soon since the sound is produced by the lens hoping off the track for a moment and not produced by teeth grinding together.