The same thing happened to a group I was with last week. We wiped after killing the final boss in Taral V and could not loot him. I filed a bug report (even though this not a bug, just poor design) asking that players be allowed to re-enter instances. I also filed a customer support ticket, asking that the three members of my group outside the instance be allowed back inside. The fourth was laying dead on the ground next to the boss.
It took an hour for customer support to respond. My group and I had given up on help by that time. Interestingly, customer support reps turned my request into a "lost item" incident despite me insisting that nothing was lost, we just wanted to loot the boss we'd defeated. They asked a couple of times "what item was lost?" and seemed to be working from an unhelpful script for their email response. I thought I spelled it out pretty clearly, but they did not seem to understand what had happened. As you can probably imagine, it was frustrating.
There are at least a few ways they could fix this situation permanently:
Allow players to respawn inside the instance Allow players to revive on the spot inside the instance Create a pop-up after the final boss that players could click to "exit flashpoint" (this would put them outside the instance and not allow them to return)