Steve @Shelton and I looked at an interesting problem a few days ago. Steve had rigged a new character of his and was SmartSkinning several joints when he realized he had been doing the SmartSkins on control bones, not geometry bones.
Why is that undesirable?
Well... control bones are created to consolidate the manipulation of multiple (geometry) bones into one (control) bone. For ease of animating. In the case shown below, TSM has two geometry bones in an upper arm. the first swings around to move the arm forward/back/up down while the second only rotates on its long axis to handle the twisting of the upper arm. this helps mimic the motion of the skin on the upper arm... the skin near the elbow is what moves most when you twist your arm.
The TSM2 arm control manages both of those bones' particular motions via constraints, but that means it will do twisting motion the first geometry bone never does.
Additional SmartSkinning COULD be done to compensate for this but... it's easier to do fewer SmartSkins than more.
So, what to do?
It is always possible to delete this undesired SmartSkin and redo it on the proper bone. That is entirely doable.
However, after some experimenting we found that some text editing could transfer the SmartSkin information from the wrong bone to the right bone.
Loading the MDL file into a text editor we searched on "smart" and paged through the instances until we found the one associated with the control bone "1 left upper arm". Smart Skins are held between a pair of OBJECTSHORTCUT tags.
We copied the name of the correct geometry bone "1 left upperarm1" (note the slight difference in spelling) in A:M and pasted it over the undesired control bone "1 left upper arm".
Then we saved the altered text file into a new model name, loaded it into A:M and tested the arm motion.
SHA-ZAAM! It worked!
Be careful not to change anything about the spacing before or after your copied and pasted bone name. That can created odd corruptions of your file.