Deep re-organizing a vault after users messing around, Or New Vault

Hi everyone!

I m quite fresh to SolidWorks and the Workgroup PDM. I went through a lot of talks in the forums but I haven't seen having the same project than mine.  I want to clean and reorganize the vault of the company because many people messed around and it is not efficient anymore.

I would like to replace the structure: Files are in many different folders (by client order number) with assemblies, parts and drawings. But parts and sub assemblies were re-used  from here and there to built new assemblies and you can imagine the references at the end.

I want 3 main folders: 1 for parts and their drawings, 2 for generic parts from suppliers, and 3  for assemblies and their drawings each having few subfolders.

Solution1: Can I  search and erase the files from the vault through windows explorer (extract all the *.sldprt for exemple), put them safe in my HDD, rebuilt the vault and then Bulk Ckeck-In in the new place as I want? Will the references in assemblies will be ok?

Sol 2: Should I just move everything like I want and rebuilt the Vault?

Sol3: Restart a new Vault from scratch with the "bulk checkIn", but I have no idea if the references will update automatically when rebuilding the vault?

Please some info or experience would be a great help...

Cheers!

SolidworksWorkgroup Pdm