I have a Owncloud server version 10.4.0 (stable) running over Ubuntu in production.
I have a new server with the Owncloud server 10.10.0 (stable), installed from scratch.
Everything is running ok, users, apps, documents, etc., but is missing all shares from the old server.
How to copy shares from the old server to the new one?
It looks like you only copied the files but not the database. This does not only contain sharing data but also file metadata, group memberships, activity history and so on.
So Iād recommend to perform a clean migration. i.e. create a database dump of your existing installation, rsync/copy your data directory and have the same owncloud version on the target server (10.4)
The migration process is well documented at Migrating to a Different Server :: ownCloud Documentation
There is no other way to get your shares migrated.
Use the very same directory path for your data directoy. It is not a good idea to move the server and the data directory a the same time (unless you really know what you are doing) If it is required to move the data directory later, please read the instructions at Manually Move a Data Directory :: ownCloud Documentation very carefully.