So SPS? Then definately not due to the skimmer. As you know sps get well over 90% of their food from thier internal zoox, the balance is absorbed and slime netting of bacteria. Most of what is in the water column are the bad guys (preditors) all thought thier are some good guys to, but it would be realy hard to make an impact on this population with a skimmer.
Don here is a thought. You mentioned the fact that the tank water got very clear. This would mean that the corals were exposed to much more light intecity. This is a simular problem that some folks get into when first starting to use ozone. They over all the bases for dealing with the ozone but forget about the water clarity issue.
Ok bact to the corals, I figure that the clarity created the corals to be subjected to alot more light intencity, which caused the zoox to begin to over process, which caused the over production of oxygen. This combined with other elements in the coral can create a super radicle oxidizer. The coral has methods to deal with this, some of which is to exspell zoox and other forms nutrilize the radical. I would imagine the smaller corals were more effected as they would have enough of the counter cure to deal with it.
On the skimmer, yes I would let it go. It sounds like the skimmer is doing a great job and has reduced your doc's and simular down to the point where your water is very clean. This makes the skimmer a great tool against biological blooms and nutrient rises or events. If you are worried you could reduce the time the skimmer runs but I would just let it go. My skimmer did the same thing after the annual WC. It shut down for almost three weeks and then began skimmer green once again and has continued to date. The skimmate is of a weaker color and not as thick in the waste pale, but IMO that is because most of the skimmate is doc.
Mike