Hi Nick,
I read all the information that you provide in
https://documentation.clearos.com/content:en_us:kb_o_upgrading_from_clearos_6.x_to_clearos_7.x/snake game as well as https://documentation.clearos.com/content:en_us:7_ug_configuration_backup.
However, I still have some problems that need to clear. Firstly, can you explain how to delete and recreate flexshares in the webconfig?
Thanks a lot!

Correcting owners and permissions will be difficult. I have no idea how you find the correct ones.

You can get a copy of the daily configuration backup from /var/clearos/configuration_backup. Obviously choose one from before your disaster. Also have a read of https://documentation.clearos.com/content:en_us:kb_o_upgrading_from_clearos_6.x_to_clearos_7.x to give you ideas of other data you may want and https://documentation.clearos.com/content:en_us:7_ug_configuration_backup. If you have flexshares and websites defined, a configuration restore won't restore the folder structure (especially the bind mounts in /etc/fstab) so you may need to delete and recreate any shares or websites in the webconfig. This won't delete any data but it will recreate the folder structure.