I'm not a lawyer....
But if you buy licensed parts, then the original copywrite owner is getting their cut. The reason that they sell these parts is to fix up your games... As far as I know, you are allowed to do whatever you want with officially licensed purchases.
Think of it this way.... what's the difference between a game that is 0.1% complete (restoring a game that is just the original flippers for example) before you're allowed to restore it (replacing 99.9% of the parts).... or whether a game is 99.9% complete, and you just need to replace the flippers for it to be complete?
You will run in to trouble though if you start making reproduction parts and a significant part of a machine that you are selling as new is made up of unlicensed reproductions.