I have 3 folders in IE favourites that I am unable to remove or delete.I keep getting a message for each folder "This is no longer located in C:\Users\Bob\Favourites. Verify the item's location and try again." But when I open C:\Users\Bob\Favourites they are all there. I cannot delete them from this folder either without getting the same message. I think this has to be a registry issue but I don't know what to do to eradicate these 3 'ghost' folders.
Second, You can try to add a take ownership to the file or folder, and try to delete it, Info about that is Here. (P.S. This is great to have for several situations.)
Third, if it is registry, Try to run CCleaner which is found Here, and It has a registry tool.
If those don't work, we can get some more information and go from there, Also, are you making sure you are running as Administrator, and that in the control panel, the display protected system files is unchecked, if that is ticked, you will see all kinds of system files that you don't want to see.