I spent along time now on my second character, and the same thing happened.

I build the geometry, build the skeleton, bind, paint weights to my liking, and then something happens. I think maybe it's because I moved stuff around like group and ungroup. It seems that I can't change the pain weights for meshes that are bound to the skeleton, they don't even show up. Like my body and head don't have weights anymore even though they move right. For instance, my left shoulder moves the way it should, so it has weights, but when i look in the pain weights tool theres nothing there for skinn clusters??

OMG please help me!

All of the things on the left under Reference are somehow connected to the things on the right. The only thing that still shows paint weights is the left boot top. I must have done somthing...