I think the zoox algae saw the skimmer being built and jumped ship
lol
I have made a number of changes in my husbandry, aquascape, flow, and water levels so I can't give you a silver bullet but i will say this:
1) Aquascape: Any Live Rock in your tank which is not recieving enough flow to blow detritus off of nor can be consistently blown off with a baster or power-head should be removed. The 1lb of LR per gallon of tank water seems to me to be another rule of thumb farse just as the Watts per gallon or turnover rate rules.
I removed about 100lbs of LR from the display and revealed several detritus traps. After removing EVEN 100lbs their was nothing but good effects on the tank. I started to see new colors in my corals after I made this change.
2) Water Chemistry: Even if PO4 is not detected anywhere in your tank, you still have it, and chances are lots of it.. Keeping your CA level up above 350 IME does more to precipitate PO4 than any PO4 stripping media.
I had been running Rowaphos consistently for months. I stopped for lazy reasons but then elevated CA levels above 350 (they were between 310&320) and again I saw noticeable color improvements.
3) Filtration: After adding filter socks and changing them out every 5 days again I noticed color improvements. I assume this is due to water clarity improvement.
4) Water Changes: After changing 70gal of water bi-weekly there were noticeable improvements in coloration.
5) FLOW: Although we all know flow is important I recently did some testing on specific browned corals which didnt have problems with trapped detritus in the base but were still in lower flow areas of my tank. After moving the "BlueBerry" above as well as a Table coral into HIGH flow areas, their colors began emerging noticeably after only a few days. A recent article talks about Zoox algae types, where they are most densly populated ect ect. I believe the cooling involved with high amounts of flow over particular SPS corals impacts the Zoox type and population helping and maybe in some cases hindering coral pigments..
Soon I hope to finish the new skimmer and reduce the frequency or need for filter socks and move to monthll water changes. We'll see how that goes..