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silicone in guitar cleaner?

The issue with silicone is how often you use it and for how long. Once a week for 25 years? You are in the toilet. Once every year for 3? Not nearly so bad. If you have it in the back of your head that one day your bass will become a highly coveted instrument, avoid it like plague. If you think it more likely your great-great-nephew will one day use it as a bow to shoot arrows? How much does it matter?
 
After some research on the intertubes, I gather that the main problem has to do with finish repair. If one gets a scratch, then it's horribly difficult to touch up because the paint will not adhere to the silicones. Also, over time said silicones will degrade and form silica (aka sand). This process is very time and use (how often you play) dependant but I wouldn't worry about this factor if you're semi-regularly applying the polish.

Silicones themselves are relatively inert chemically (just think caulking and how often you have to apply that) and the silicones are in such low concentraion (~5-10%) which can't really do much in low dosages to the guitar.
 
p.s. wax and grease removers will not completely remove a high quality silicon product! using two wipe downs with wax and grease remover, one after the other, is just the beginning step in trying
to avoid a silicone contamination issue. this is an every day battle in the refinish business and i wish it was that simple! as you are sitting there reading this forum i would bet there is silicon on
your hands right now as well as your clothing, hair and almost everything you touch.

Guess Ive been lucking, In the 10 years Ive been in the refinishing business Ive never had a contamination issue. I wash the car with soap and water then wipe it good with grease and wax remover before starting any work to keep the sandpaper from grinding anything into the paint. Then wipe it down between ever step, That means before filler work, before primer, before sealer, before paint.