So i’ve already done the wow folder stuff.
My character (ianai-medivh) is having some messed up phasing issues where the portals are fake, there is no meeting stone and most any entities (non map doodads) are just… gone.
its isolated to the innards of the structure and the space near the crags/cracks around it
So by wow folder stuff, do you mean a full UI reset?
The portals aren’t exactly fake, you just don’t currently have access to them in your present state. 
Phasing issues are rarely caused by the UI but most often by being on a quest or in the middle of a quest line that phases the area to match the story.
In this case, it looks like you may have started a quest line that involves the Nexus. You completed “A Fresh Trauma”, but didn’t pick up and complete " A Bolt from the Blue".
Doing that should return the area to normal.