pkextractor fails to handle duplicate hash entries within trunk.txt
Both client/res/maps/nexustower/nd_nexus_tower_7x1_audio.lvl and client/res/maps/nexustower/nd_nexus_tower_12x1_audio.lvl have an original MD5 hash of c4600a972a4154bb1cb67c8493ba1c16, due to the hash being used as dictionary key to map to filename, this means that pkextractor "forgets" that client/res/maps/nexustower/nd_nexus_tower_12x1_audio.lvl exists when it reaches client/res/maps/nexustower/nd_nexus_tower_7x1_audio.lvl within trunk,txt.
There may be other files affected, I have not tested to that extent.
Hmm, that's a good catch. Unfortunately, with the way pkextractor works right now, there is no simple fix for this - it would require a rewrite to go through a different index the game uses. I'll try to look into it when I've got time, but it'll probably be a while.