To answer the question. Yes you can turn slotted or drilled rotors. It's best to use new bits, and take light cuts. If you see chatter marks after a slot. You either need to change the cutting bits, or take lighter cuts, or both. The chatter marks are the bit bouncing across the metal. Some places don't like doing them because of ruining the bits. They ruin the bits by taking heavy cuts.
As for your problem. Sand the rotors down, and rebed the pads.
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