Hello Kayaoo,
When you say that you cannot get it to work, what specifically do you mean? Do you get an error?
The Save.Instrument method will not delete the existing VI on disk, rather the Save a Copy input determines whether or not other VIs that are in memory at the time will relink to the VI at its new location. You'll still need to delete the original file once you've resaved it elsewhere.
You may also want to consider moving your VIs to lvlibs, particularly if they're already static libraries intended for reuse and the lower-level functions don't need to be or shouldn't be exposed in the project. Refer to this document for more information:
White Paper: Best Practices for Sharing and Reusing LabVIEW Code
http://www.ni.com/white-paper/9648/en/
Regards,
Tom L.