Sometimes we want to add folders having duplicate files (like shaft, plate, etc.) in different folders. I tried this method on small sample data and it works.
1) Ensure that vault allows duplicate files with same name (vaultAdminTool->Vault->FileTypes. RightClick->DuplicateFileNameSettings. Allow duplicate file names)
2) Add all the new folders to an empty folder in the vault
3) Check-in the folders
4) Use search tool (with scope as new data location) for the common file names. You will see many files with same names.
5) Modify the file names and their references will be updated. You don't need to checkout the files to update references.