if it's the same parts they have the same ref so you have a part that is multiplied by the number of parts and that you should find it on your monenclature once you have redone the design of your assembly validate and saved
I don't really understand the question, are you talking about the nomenclature of solidworks or a Windows folder tree?
If in the solidworks BOM a part appears several times it is because you have a tabulated BOM and that the components are in several sub-assemblies for example, but I don't see the connection with the Windows folders.
In any case one part = 1 file, if you have the same part in several different windows folders there will automatically be a problem at some point since when opening the solidworks assembly will put you an error message concerning the internal ids of the documents.
On all the software running on Microsoft OS you can't open in the same application two files saved in different places but with the same name!
I'm talking about the windows folder tree, the idea is to have the same folder tree as the nomenclature that exists on another software for production management. We would like to have the same nomenclature at the BE as well as at the production which is not the case today!!
So your current problem is just to move solidworks files in a Windows folder tree, right?
What exactly is the problem?
In any case I strongly advise you not to duplicate your solidworks files, as I said before a name = a file if you try to recreate a Windows file tree with files with the same name in different folders it's the error message guaranteed, but above all a risk of real error at the time of production ... imagine if your two parts with the same name have a different geometry (one user modifies one file and not the other for example)!