Can the files that are imported as assemblies with many parts just be saved as a multibody part file (.sldprt) or do you require mates for kinematics? If you can save some of these imports as part files it should greatly reduce your file count overhead and confusion.
If I understand your question, you want to purge your folders from old and unused files.
Probably your best option would be a "pack and go" command, called from the assembly file.
Just save every file required by your top-level assembly to a new folder (or zip file) and pass that to your contact.
An alternative, altough quite dangerous and not suggested (ok, we all do this now and then, don't pretend) is to open the top level assembly, resolve all the parts and leave SW in background. Now go to the model folders and move *all* the files to a "trash" folder. When windows prompt something about the files being in use, just "ignore all" and there you go, the folders has been purged.
thanks . pack and go works well, / im not sure anyone knows this command in our company :/