I think I understand what your saying, I added this attachment so you could get a better idea of what I am trying to describe.
If you look at the very first ST32 file (ST32-00000) it is in a Design folder that you cant see.
In the ST32-00000 is another design folder which is wrong, the problem is a lot of the files in this location are the ones linked to the drawings, but not their higher assemblies.
It should just be the ST32-00000 file then all its sub folders. EG. ST32-10000, ST32-70000
hopefully this makes things more clear.
Thanks,