I am running owncloud 9.1.1 right now ... and i would like to start a brand new FRESH server.
What i am planning to do is: install new vm, install owncloud, link it to LDAP (so it adds all my users) and then copy their home dirs from my old owncloud server to the new server and then turn on the new server. I am afraid of losing my users file. Say they try to sync it wont delete any of their files that are already stored on their computer would it?
Not sure, why you cannot use your current setup. In a new setup, all your users will have to sync their data again. I'm not really sure how the clients react, if they prefer the server version, if they try to upload the existing content. I would test this scenario with one account for testing first.
Cleanest way, set up a new server under a new address and ask users to add this to their client. You can migrate their data, and when everything works, they can just delete the old account on their client.