I think I am having the same issue as you, the lighting builds perfectly several times and then all the sudden breaks. Lights and shadows no longer have any detail and things look awful. This is the second project I have had this happen to and can’t figure out why this is happening. I have done everything you listed above including migrating levels over to a new project (this worked once, but not after the second build and has not worked since), deleting the intermediate folder (after making a copy of course) and even tried building in the new 4.13 version. Nothing seems to work. It doesn’t happen with every project though, and it seems totally random - fine one build, broken forever the next.
In other words, I am adding my vote for this being an issue.