Hi,
The problem is that ownCloud does not automatically propagate changes from external storage to the sync client. However, we have an app and a service exactly for your issue. It’s called Windows Network Drive and WND Listener. The listener listens for changes and propagates them to the sync client.
https://marketplace.owncloud.com/apps/windows_network_drive
You can use occ files:sync as a cron job to scan your system for new files in regular intervals. This is a workaround and can last a long time depending on the amount of your files.