1-2mm of rust is quite a bit on a rotor to take off. If you had to take that much off by hand it's unlikely the rotor would be true afterwards.

When you get the different "sound" does it feel like it grabs any more/less than the rest of the disc? If it does you may get uneven compound transfer to the disc and subsequently a wobble when you brake. You can put them on the vehicle and see what happens, but you may end up having to get them refinished and/or cut.

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