Eventually I restored ATV and wiped the external HD (but copied shows and movies to another).
UPDATE:
TV shows now appear under “TV Shows” in sapphire. after I pressed import again (for the sack of it!) they turned up! Still no movies though
I have some screen shots of the roots from the FTP program i use called transmit. Maybe people know if the files here are right??
Can you check to see if the latest version of Sapphire is installed? Updates can be downloaded through the Maintenance > Manage Plugins menu.