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Okay first I would inspect your brakes thoroughly and try to find if there is a more serious issue behind the noise you are hearing. Is this noise occurring only when doing a certain thing with the car? (Under braking, when turning, etc) A recording of the sounds would be great too if you're unsure if the cause of the sound is actually just the pads needing bedding.
You also have to regularly bed brake pads. The transfer layer goes away over time.
You should regularly inspect your brake pads & calipers anyways. You'll be fine if you swap pads but reuse the rotors. You'll have to bed the new pads obviously.
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