Lapping will not decrease peformance. If you get it so smooth, then don't use AS2. Its thermal conductivity is only ~1/50 that of pure copper. The reason we use thermal paste at all is because its too difficult to perfectly lap a sink.
Furthermore the kind of lapping we are talking about here with sandpaper and a piece of glass is fairly crude. Take it to a shop or lab and they can smooth it down to the equivilent of many thousands of grit with solutions and real equipment.
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