Someone mentioned allelopathy (coral chemical warfare) in an earlier post, which is one of the first things I thought reading through your thread. Then this came out last week:
Coral War Photos — Advanced Aquarist | Aquarist Magazine and Blog, which is I thought I would share with you. Not invisible chemicals, but actual stinging tentacles that reach out to neighboring corals that cause damage.
I've lost a few sps corals from bleaching at the stem this past year as well, and so have done much reading on it. I found this website of links to have the most comprehensive list to help to figure out what might be going on:
Coral Diseases and Parasites
One last link, older article, but found it also useful, "Old Tank Syndrome", does it really exist?:
Feature Article: Old Tank Syndrome — Advanced Aquarist | Aquarist Magazine and Blog
Any updates? I know you are putting in LEDs, been following that thread also, but wasn't sure if you have been able to stop the loss.