I don't see a problem with cutting back on protein skimming hours, especially if you don't have nuisance algae problems or high nutrient levels. If the LPS that you want to focus on are night feeders like Acanthastrea & Lobophyllia then maybe skimming during the day will be better for SPS and not skimming at night will offer more available food for night feeding LPS.
What are your nitrate and phosphate levels now? While protein skimmers are very efficient at removing protein, they will allow heavy metals to accumulate. If your nutrient levels are above zero, it's possible that the LPS are adversely affected by heavy metal accumulation.
The other approach would be to maintain your filtration as is, and do more indirect feeding with Phytoplankton.
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