Low nutrient levels will cause a decline in LPS health, but it is not necessarily caused by your protein skimmer. It is more likely an issue tied to nutrient export such as water changes, algae harvesting, and other chemical filtration methods like carbon and ion exchange resins.
LPS & SPS don't readily mix in nature, so our expectations are generally over-optimistic when it comes to a mixed captive reef. Target feeding may be the only compromise of supply and demand.
There is some debate whether or not carbon is the limiting factor for coral health and growth. My guess is that carbon dosing fosters the growth of microorganisms that feed corals and consume nutrients, rather than bacteria that consume nutrients.
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