Went to the Abandoned Border Tower in the bridge of theives to do an in depth long term RP/Research mission.
We looted the chests... and all the loot came back after a time? Uncertain if this is a bug or intended. I know there are some chests on shared maps in say, Cordor or Andunor that likely will respawn even with people in them since they are so busy (Here's looking at you, Andunor hub chest) but this might not be good in dungeons.