You may very likely have bent the thin metal backing plate behind the brake rotor. That will cause the backing plate to rub against the rotor and make an awful grinding noise. Its not too hard to reform the backing plate away from the rotor.
The brake caliper should not touch a rotor ever. There is a metal backing plate on the brake pad that can rub the rotor if the pad wears thin enough.
You can only have them turned a few times until they are too thin to be considered safe. Usually this thickness is stamped on the rotor.
Rockets into space poke holes in it. Aircraft cause it to thin. Combustion exhaust and cooling towers cause it to thin. Older refrigerants cause it to thin. Cutting down forests causes it to thin.
If your brakes are squeaking, that means the pads are wearing thin. When you hit the brake pedal, the pads push against the rotor to create friction and slow down the vehicle. Over time these pads wear away, and when they get thin enough they make a squealing noise. This noise notifies you that you need to have new brakes installed as soon as possible. If you keep driving without replacing them, the pads will eventually wear down completely and then every time you hit the brake pedal metal will scrape against your rotors. This can be very damaging and dangerous, so when the brakes start to squeal have them looked at right away.
If the brake pads are not worn out check the backing plate. It is the thin metal plate behind the brake rotor, sometimes it will get bent and rub on the brake rotor.
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I'm pretty sure you are talking about the spindle. If equipped with a thin piece of metal that is a dust shield.
If you're changing the brake pads and there is too little rotor thikness to turn it, it should be replaced. If the rotor is warped and is too thin to be able to turn to remove the warping, replace it. If the brakes "pulsate" when you use moderate brake pressure, the rotor is warped.
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Rotors that have been marred up by brake pads can be turned on a machine and made like new. You can only have them turned a few times until they are too thin to be considered safe. Usually this thickness is stamped on the rotor.