This bug indeed a little tricky.

My current attempt to fix this looks like

diff --git a/dialogs/Duncan.dialog b/dialogs/Duncan.dialog
index 1f5fced..5d12443 100644
--- a/dialogs/Duncan.dialog
+++ b/dialogs/Duncan.dialog
@@ -35,6 +35,7 @@ Beginning of new chat dialog for character="XXXXX"
        end
 
        if (has_item_backpack("Pandora's Cube") > 0) then
+               add_cookie("has_pandoras_cube")
                next(60)
        else
                if (has_cookie("koan_spared")) and
@@ -187,25 +188,27 @@ NO_TEXT
        if (has_cookie("koan_spared")) then 
                tux_says(_"I could not find him anywhere in the desert. I don't
think he is there anymore.")
                npc_says(_"I see.")
-               end_quest(_"Doing Duncan a favor", _"I lied to Duncan about not
finding Koan.")
-               end_dialog()
-       end
-       if (has_item_backpack("Pandora's Cube") > 0) then
-               show(62, 63)
+               if (has_cookie("has_pandoras_cube")) then
+                       tux_says(_"However I think I found the thing I was
supposed to get you?")
+                       show(62, 63)
+               else
+                       end_quest(_"Doing Duncan a favor", _"I lied to Duncan
about not finding Koan.")
+                       end_dialog()
+               end
        end
        add_cookie("koan_quest_done")
        show(64)
 </LuaCode>
 ----------------------------------------------------------------------
 
-Nr=62 Text=_"Yeah. I got him. I think this is your cube."
+Nr=62 Text=_"I think this is your cube."
 <LuaCode>
        npc_says(_"Yes. I appreciate your help.")
        hide(62, 63) next(69)
 </LuaCode>
 ----------------------------------------------------------------------
 
-Nr=63 Text=_"Yeah, I got him. Now, what is this big cube that you had me carry
all the way here?"
+Nr=63 Text=_"Now, what is this big cube that you had me carry all the way here?"
 <LuaCode>
        npc_says(_"Just a memento from a friend.")
        npc_says(_"A little more than a portable end of the world, which I am
looking forward to disassembling and learning its secrets.")
diff --git a/map/events.dat b/map/events.dat
index 81546ff..90207bb 100644
--- a/map/events.dat
+++ b/map/events.dat
@@ -354,6 +354,26 @@ Silent=1
 </LuaCode>
 * End of trigger *
 
+
+
+
+
+* New event trigger *
+Name=_"Koan_alive_check"
+Trigger entering level=0
+
+<LuaCode>
+if (npc_dead("Koan")) then
+       add_cookie("murdered_koan")
+end
+</LuaCode>
+* End of trigger *
+
+
+
+
+
+
 ##############
 ## Level  1 ##
 ##############



however, it still lacks some more testing and probably a few more tweaks