You're referring to a blank item in the media library view, correct? At the top of the window, there should be an icon that looks like a circular arrow. Pressing this item should rescan your folder and remove the missing item. Alternatively, you can also delete the item directly in HereSphere, which will automatically remove the saved video settings as well.
If you're using XBVR, you'll need to update/rescan your folder in the XBVR UI so the XBVR database gets updated after deleting a file. You can also delete files directly with HereSphere while using XBVR. Just make sure the delete file toggle is enabled in the XBVR UI options (under player options -> heresphere).