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I am not 100% sure, what caused the shuffling of the bone indices, but the old exporter (from which mine was derived) used the order of the vertex groups, the current version of the blender exporter (ogre homepage) sorts the bones by the order they are in the armature (some sort of one bone then its children, then the next bone).
What we could do, is use the new sorting and then we have to re-export all existing clonk meshes (I don't know how many there are?). Or we try to get an exporter working, that maintains the old, a bit strange, order.
I already wanted to put some time into this, but haven't had enough time for that yet.
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