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:
mv commands to move the files around.
To have OwnCloud see your file changes, go to
sudo -u www-data php occ files:scan <USER>
Let your OwnCloud scan and then be happy.