Hot gas phase recycling cycle
When advanced atomically perecise products start to get used diamondoid scrap will start to accumulate. Through sensible system design with direct recycling of microcomponents the rate of scrap production could be held low but it will undoubtedly accumulate.
To keep the waste from the environment it should be thermally disintegrated. See: "diamondoid waste incineration"
Gasses might be directly processable with advanced forms of tooltip chemistry. Pure hydrocarbon diamondoid waste won't produce solid ashes. For ashes from silicon or metals liquid phase bulk chemistry might be needed (possibly as small as desktop scale).
Lessons will be takeable from the improvement of conventional mining and post processing with AP technology. See: "improved mining".