I was thinking of shutting my skimmer off during the lights out cycle. Logic being that corals feed at night. With the skimmer off, there will be more food consumed by your corals and less ending up in your skimmer.
Turning off your protein skimmer is not going to increase the availability of food in the tank. The blanket statement "corals feed at night" is very misleading. Corals will feed any time there is food in the water, whether it's daytime or nighttime.
It's true that many corals have evolved the behavior of increasing polyp extension at night in an effort to collect *more* food, but they have the ability to feed at any time of the day.
Increased polyp extension at night is simply an evolutionary response to the fact that corallivores (animals that eat corals) are mostly inactive at night, thus allowing corals to increase polyp extension, and collect more food, without such a high risk of predation.
I dont think that much slime and warfare will occur in that space of time to hurt your corals. I have tried it and my corals are fine....Tank is thriving.
First of all, "I [don't] think" is always a bad way to begin a statement. What facts or observations are you basing this on?
If you look an any of the hundreds of research papers that discuss the production DOC-lipids (mucus/slime) in scleractinian corals, you'll find that corals have peak mucus production when sunlight is the most intense.
Meaning that most slime production occurs during the daylight hours.
If you were to shut off your skimmer right as the lights turned off, then whatever slime has been produced and accumulated during the daylight hours, and hasn't been removed by the skimmer, will remain in your water until it either decomposes or is removed by the skimmer when it resumes operation.
Many of the chemicals used for allelopathy ("warfare") are contained within, or are produced along with, coral slime. Meaning that there is the potential that you could very well be negatively affecting your corals' growth and health.
Another important factor to consider is gas exchange. At night, zooxanthellae switch from photosynthesis (CO2 to O2) to the opposite process, respiration (O2 to CO2). This then puts more demand on your tank's dissolved oxygen concentration, which can potentially lead to hypoxic (low oxygen) water conditions if sufficient gas exchange is not maintained.
So, is it really a good idea to be turning off your skimmer, a vital source of gas exchange in most tanks, just when gas exchange becomes the most crucial for the well being of your animals? Probably not.
As for your individual case, isn't it possible that your corals could be "thriving" *despite* turning off your skimmer at night and not necessarily *because* you are?
Is there any disadvantage to only skimming during the 12 hour period?
I currently have the skimmer on the same timer that runs my fuge lights which is opposite of my main tank light cycle.
I would recommend running your skimmer 24/7. In addition to the disadvantages I've mentioned above, repeatedly turning your pump on and off can cause unnecessary wear and tear - potentially causing your skimmer's pump to fail prematurely.
If you're worried that it's pulling out the food that you add to your tank, then simply unplug it for a couple hours after you feed. Other than that, and maybe saving a couple dollars a month of electricity, I can't see much advantage to running it only 12 hours a day vs. 24.
