I've been soloing team missions. The last one I did, I killed about 15% of the mobs before heading to the boss room. The boss was a little too tough, so I left that level and killed a bunch more mobs, leveling twice in the process. After having killed about 85% of the mobs, I was low on ammo, so I left the mission to resupply. When I got back to the mission, I killed the rest of the mobs before heading back to the boss room. When I got there he was gone. I still had 4 hours remaining to complete the mission. I picked up the object in the boss room and got my token and reward items.
Three missions ago, I killed all the mobs and then headed for the boss room. He caught me by surprise hitting me with a nano that did over 200 damage (I was lvl 22 with less than 600 max health), killing me. After reclaiming my stuff and getting over rez shock, I went back to the mission. Again, no boss in the boss room. Time was still left to complete the mission, which I did, getting my reward.
The only reason I did these team missions was for the boss loot. I'm very disappointed the boss mobs were gone both times I returned to the boss room.