If you upload files to an owncloud server via FTP, SCP or some other tool, the owncloud server at first does not notice on its own, that new files are present.
You can however, trigger a manual refresh via the command line...
A php script from owncloud can be triggered as www-data (webserver) user:
Go to your owncloud folder:
cd /var/www/owncloud (just an example)
Change to the www-data user:
su -s /bin/bash www-data
Execute the php script:
php console.php files:scan --all