I added a new source to my movies file list. The source I added was a whole drive (which I added twice by accident) and had some unwanted stuff on it so I moved all the movies to a single folder on that drive, added this to the sources and then went into ./kodi/userdata/sources.xml and deleted the reference to the whole drive. There was only one set of XML data for this drive which when deleted removed one of the sources in the osmc gui.
The other instance of this source remains, but when I open sources.xml it is not there. why is osmc showing this one still and how can it be rmoeved.