I think some confusion may have crept in here, that advice is good for schematic libraries, but does not make sense for footprint libraries. Probably, you should not be allowed to enter two libraries with the same nickname, but never mind.
The recommended approach is to delete the github entries if you do not intend to use them, moving them is not necessary, which is what you have discovered.
My current faq entry looks like this:
How to install local Footprint libraries
(Tested with Kicad 4.0.2)
Using KiCad:
N.B this gets latest footprints from github, may be incompatible with your currently installed data.
- Start Kicad
- Open pcbnew
- Select menu option Preferences->Footprint Libraries Manager
- Delete all the libraries in the Global Libraries list
- Click “Append with Wizard”
- Select “Github repository”
- Enter “KiCad EDA · GitHub”
- Select “Save a local copy to”
- Click browse and select a new folder e.g. “c:\kicad\footprints” (create folder if it does not exist)
- Click Next
- Click Select all
- Click Next
- Wait while libraries are checked
- (some libraries may be marked INVALID, not sure why…)
- Click Next
- Select “To global library configuration …”
- Click Finish
- Wait while libraries are downloaded.
- Check - open the Footprint Libraries Manager, you should have about 84 libraries in the list with the local path specified.
- Click OK
- Close Kicad and restart
- Note: KISYSMOD will still show default location, this does not matter.