It's your pathing. First should be worldgeneration, not biomes. Remove the first biomes in your path and it should work now.
Also, if you are setting everything to zero, you can do it by two lines
<set xpath="/worldgeneration/biomes/biome/@lootstage_bonus">0</set> <set xpath="/worldgeneration/biomes/biome/@gamestage_bonus">0</set>
you can also just remove most of the code and do this:
<set xpath="//@lootstage_bonus">0</set>
That will change all instances of lootstage_bonus to 0.