I have barely just installed Zentyal and don't run it yet, so I can't say much about the Zentyal side of things (I guess just remove the ACL wherever you applied it, so Zentyal doesn't reapply it).
If, however, you have a backup of the file system, you can look up the folder permissions in the backup and re-set them on the command line or through the GUI, if you have one.
If you don't have one, you'll have to do a bit of work. Through either the command line or GUI, start by setting ownership and permissions of only the /home folder to root:root and 755 (chown root:root /home and chmod 755 /home).
Then for the individual user folders, the scheme is always the same: /home/someuserfolder itself has permissions 700, the files below vary according to what the user did - 644 is default.
The folder and all files below are owned by the user and and belong to the group "domain users" of your domain.
Run the following commands:
getent group | grep "domain users" - this will give you the name of your domain users group. It'll be in the Format NETBIOSDOMAIN\domain users.
getent passwd | grep "/home/" - this will give you a list of people who (may) have folders below /home. You should see all the usernames of your domain in the format NETBIOSDOMAIN\username as well as the home folders assigned to them (the foldername ends before the next colon, e.g. out of /home/username:/bin/bash, /home/username is the folder).
For each user, run the following commands, switching out NetBIOS-domain and username as appropriate:
chown -R "NETBIOSDOMAIN\username":"NETBIOSDOMAIN\domain users" /home/username # this will recursively reassign /home/username and everything below to that user. If the previously output user list shows a different home folder than /home/username, alter that part appropriately.
chmod -R 644 /home/username # this sets the folder and everything below it to to the default permissions of rw-r-r
chmod 700 /home/username # this corrects the permissions of the home folder itself to only be visible to the user
This is only the system side of things. I don't know what else Zentyal does on top of that. If any of those folders are mounted through a network, you will also have to check the Samba permissions.