1. If you kill Nere before interacting with Philomeen when you get to her she just stands there looking away and you cannot talk to her. You can however pickpocket both the vial and barrel of rune-powder with failures eliciting no reaction from her.
2. If you Kill Nere before interacting with Skickpit he is standing alone when you come upon him, however when you talk to him the scene with Ward Magmar plays out with the two Duergar as if they are still there. I selected 'Attack' after a few dialogue choices and it left the dialogue screen to just Skickpit alone again and the next time I talked to him he told me I did it and gave me a wyvern poison.
3. If you go to turn based mode before triggering the explosives where you free Nere, Meerna and Beldron are standing alive in front of Nere in the poison cloud room after the explosion. If you get close enough the cut-scene where Nere kills Meerna triggers but instead you can start combat from bow/spell range bypassing that killing. However she "POOF" disapparates on the first damage Nere takes and her brother still laments her death. Just seems a bit weird and wonky still.