OwnCloud works well for small changes and uploads, but moving or renaming a folder that is a few gigabytes will be troublesome. OwnCloud might think you are actually deleting and then reuploading the files.
You can try WebDAV for reasonably sized files and folders to avoid OwnCloud screwing up the syncing, but you have a better option.
First, disable sync clients to avoid unwanted error notifications.
If you have access to the server, you should ssh into the server. Go into the user’s files directory:
/var/www/owncloud/data/<USER>/files
Use mv commands to move the files around.
To have OwnCloud see your file changes, go to
/var/www/owncloud
and run
sudo -u www-data php occ files:scan <USER>
Let your OwnCloud scan and then be happy.
Man and Keyboard 
Worked as a charm, thanks!
Worked as a charm, thanks!
Does not work on owncloud9
OwnCloud might have changed this command, but it would be there in the documentation.
sudo -u www-data php occ files:scan
Thank you, this help