I came across an issue with owncloud where I had manually placed files in my user directory but the files were not showing up in owncloud. I found from here that you can access the owncloud console directly and trigger a re-scan of your files.
To trigger a re-scan, open up a terminal session to your owncloud server and run the following command:
php /path/of/owncloud/console.php files:scan --all
This will trigger a re-scan of all files for all users. You can replace –all with a userid if you just want to scan a specific user’s folder instead.