Owncloud 9.1 --> 10:Waiting for activation of the extension object owncloud:

Are the files also gone in the filesystem (/var/lib/univention-appcenter/apps/owncloud/data/files) or only in Owncloud?

Yes, also on file system.
I still have them on my local harddrive synchronized, but how can this happen?

Kind Regards,

Tobi