So the day after finishing my green fire quest i decided to go into BT because i wanted the green fire dagger, Shard of Azzinoth. When i get in there I am still phased into the scenario version of BT and cant even use the exit to leave. My hearth was on CD so I stuck sitting there being able to go past the area Naj'entus is in because the grate is closed. I did however find out that beyond the entrance there is a replica of half the area outside BT out there, minus the temple, with a bunch of weird and missing textures.
tl;dr BT is busted for you if you do this quest/scenario it seems.