Depending on your DPS, you can push past the 3rd Kephess clone by damaging Brontes to the 50% mark (thus you only get 2 Kephess'). This will give your team much less orbs to deal with and you can also Leg Shot (to immobilize them) any of the orbs to allow for more time as well. The orbs swapping has happened to us as well, but I don't know of any good solution to deal with that outside of just having your team be very aware when they need to move out of the raid to eat their orb. Good luck.
Thanks! We'll definitely keep that in mind.