Right click the part in your folder and choose properties. Then click hidden. If you ever need to find them again you can show all hidden files in your folder options in windows and change the status back to visible.
Create another folder in your Library folder, maybe name it Old Library parts. That way when someone opens an assembly where the old part was used it will prompt them to search for the old part, and in some cases you may want to replace the old component with the new component. I think that would be a good way to make sure your main assemblies would be updated...
You could use Solidworks Explorer and use the move files command.
Move the older version file using this tool into another folder, say an archive folder, and then you'll have the new version in your design library and the older version still with it's references to where it's used maintained.