@Allnarta - I think I may be able to help. Sometimes Blender retains data from the old skeleton even after you've deleted it.
Meaning that once you delete the old skeleton/nodes (SceneRoot) then import a new skeleton, Blender will rename the new skeleton to SceneRoot.00 (or .01, 02, etc).
The only way to prevent this that I have seen, is to save your project/blend file after you delete the original skeleton, then exit blender and reload it. It seems that saving/reloading is what fully purges all references to the old skeleton.
I tend to do this a couple of times in a row to be safe. Its annoying, but still quicker than dealing with the hassle of importing the skeleton only for it to be renamed.