So I've got an update!
After doing a few water changes, buying Hanna checkers for alkalinity and calcium, buying new, lower alkalinity salt, keeping my pH in check (average of 8), stopping my GFO/carbon reactor to stop removing nutrients, my reef tank was still in bad shape and getting worse.
Well today I discovered another issue! My Apex salinity prob was off and my (backup, you know 'just in case') refractometer which I calibrate everytime I use it was also incorrect, because the calibration solution was wrong!!!!
I only discovered this after buying new calibration solution for the probe. When I stuck the probe back in the aquarium and got a reading of 42.2 ppt I thought I made a mistake calibrating it.... Nope. Just my bottle of 35 ppt solution was extremely wrong!
So now I begin the slow process of bringing the salinity down and hopefully stopping this from getting any worse.
My stylophora is almost completely white, it's shed all of it's flesh and only a few of polyps remain on the lower part of it.
I'm hoping this is the last thing I find wrong. I've definitely learned to not trust my Apex.