The title is... not helpful at all, but if you import mesh A, and then import mesh B (which is made to work on mesh A), while mesh B has bones mesh A doesn't (such as jigglebones), either Blender says "X vertices weighted to invalid bones" if Append to Existing Model is checked, or one has to manually remove old bones on mesh B and re-parent new bones on mesh B if Append to Existing Model is unchecked, since joining skeletons/armatures just adds ".001" and such to bones on the first-selected skeletons/armatures with the same names as on the last-selected skeleton/armature.

So here I bring a suggestion: A tickbox to choose whether to automagically add the new bones to the old skeleton/armature, if new ones are found while importing another SMD/DMX mesh (with Append to Existing Model checked).

It can be grayed out if the old skeleton/armature has keyframes, if that won't be compatible.