Worked with some folks in QA and at Arkane to answer some of your questions and provide some news tips.

Does killing an assassin in the prologue count?
No.

Does killing dogs count?
It only counts against clean hands.

Does using a sleep dart on Lord Shaw during the duel count?
No.

Do kills prior to dying and restarting at last checkpoints count?
They should not. Reloading a save should restore the stats you had when the save was made.

Do unconscious bodies that disappear due to polygon counts / memory space count?
No. Only if they’re actually killed (by water, rats, etc).

Do discovered unconscious bodies count?
Detection of an unconscious body would count against achievements relating to detection.

Does poisoning the elixer for Granny Rags count?
It greatly increases chaos, but that's all.

Does stunning the gentlemen callers count?
If by stunning you mean sleepdart/choke, you should obey the normal incapacitated NPC rules.

Does the game have to be played on normal to activate these trophies? (I played on Hard).
Difficulty should not matter

Does choking out the executioner count?
He should obey the normal incapacitated NPC rules.

Does installing patch 1.01 have an affect? Should I reinstall and go back to 1.00?
No, you should use the latest title update.


And for more "Knowing is Half the Battle" fun. Check out these tips...


Situations that could lead to an NPC being killed inadvertently:

• Sleep Darting or Choking out an NPC and having them hit an object when falling, causing death
  
• Sleep Darting or Choking out an NPC near a ledge and having them fall to cause death
  
• Sleep Darting or Choking out an NPC and having them fall into water will cause drowning death
  
• Sleep Darting or Choking an NPC and allowing them to fall down a long flight of stairs will sometimes cause them to die (possible with the stairs in the Overseer building)
  
• Placing an unconscious NPC in water, or even near shallow puddles, can cause drowning death
  
• Placing an unconscious body on un-even terrain near water can sometimes lead to the NPC slowly moving and falling into water, which would count as an NPC kill (in Prison Sewers for example)
  
• Rendering an NPC unconscious near a damage source (such as a fireplace or lit grill) may cause the NPC to take damage and die
  
• Leaving an unconscious NPC in the middle of the street or alley, where rats have access to the body, can result in clean-up which will count as a kill for the player
  
• Accidentally casting Devouring Swarm near an unconscious NPC could cause the rats to clean up the body, counting as a NPC kill
  
• Accidentally casting Windblast near an unconscious NPC could cause damage leading to NPC death
  
• Having a Grenade, Springrazor or Whale Oil Battery explode near an unconscious NPC could cause splash damage resulting in NPC death
  
• Throwing an unconscious NPC into a Wall of Light, or near and Arc Pylon would incinerate the NPC and count as a kill
  
• Leaving unconscious NPCs in the area around the large door on which the player places the explosive device in Prison will cause the NPCs to die when the device goes off. This includes in and around the nearby dumpster and behind the consoles and gate switch across from the door on the upper level.
  
• Rendering an enemy unconscious while fighting a nearby Tallboy can cause the Tallboy to stomp at the player, essentially killing the nearby unconscious NPC in the process
  
• Rendering an enemy unconscious and having another enemy throw a projectile (such as fire bottle or grenade) at the player, can kill the nearby unconscious NPC
  
• Leaving an NPC unconscious in the Brothel Steam room may cause “bite” damage due to hagfish in the center pool, killing the NPC

Sleep-darting Granny Rags counts as a kill.