@BJH
Again, perhaps a grasp at straws but here is how I have my server setup...
Both cops & owncloud are directly under /var/www
Owncloud data
is not in the owncloud dir... I have a vague recollection of reading an advisory to locate your data elsewhere
Mine is...
/data/owncloud/username/files/ under files , I have my 8 individual
Calibre dirs which I sync using owncloud with 8 Calibre libaries on my laptop.
With in each of these is the metadata.db
This all work fine......for what it's worth
Cheers,
TC