Models reset when another model is bonemerged to it.

[Sounalius]

So bonemerging one model and adding things (sub-materials, bones, pretty much anything that changes any feature about the model in any way), then bonemerging model two to model one causes anything added to model one to be completely negated and any properties of model one cannot be changed. (ex. Size, bone positioning, Alpha)

[DBotThePony]

Limitation of source engine, drawing children force draws the parent, and if you refuse to draw the parent (using hooks), children will not be drawn too.