Currently we check for a cookie to know if Koan is alive or not.
       if (has_cookie("koan_spared")) then 
which is the actual problem since we don't give the cookie when we "manually"
kill him.

I think the issue can be easily fixed by replacing
       if (has_cookie("koan_spared")) then 
with 
       if (npc_dead("Koan")) then
which directly checks if Koan is alive or not.