Can you kill both of them in one run?
If you cant, why are there two in there?
You need to have a good party to kill both in time. 
Yes you can. Aslong as you have a decent group and a couple of people know what direction to go first.
You have to kill mineloader first then you can kill endboss. If you kill harpie first since it is “endboss” of the dungeon it will end.
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If you’re running
-without a cleric but with a good tanker
-with a cleric without a tanker
-with a cleric and tanker
you can run both of them (mineloader then harpeia) as long as you know the route to take.
If you’re running without a cleric or tanker just take the harpeia route because either you aren’t going to make it in time or by the time you reach harpeia the number of hairstrands remaining on your scalp would have drastically decreased due to the number of hair pulls you just undergone.
full party of any composition should be able to complete full clear of that dungeon if you proceed with care. Did it with only me and my friend (duo) as 2 mages in iCBT2. Me was pyroC2 - linker - thauma, he was pyro2 - ele -sorc