I'm adding in new users via a CSV and they keep getting blocked? 

If a user does not exist in your AD but has been added to the Intranet by uploading a CSV file, then the profile created will be deleted on the active directory next sync.
 

An LDAP user account has been removed from the syncing domain group but they exist in the system as a blocked account?

The LDAP sync in Claromentis will never delete accounts or any groups they were a part of (if these came from your Active Directory)

Instead, the system sets any profile no longer syncing to blocked status. These can be found by performing an advanced search in Admin People.

Blocked accounts mean the profile can be re-activated at any time (by adding the user back into the syncing domain group) so its personal information can be retrieved.

If you need to entirely delete these profiles, this needs to be carried out manually in Claromentis, via CSV, or individually.

How do I sync managers from LDAP for the org chart?

When pulling in a user DN to set up the synced fields the following two options will also appear below the list of synced fields. 

From here you are able to sync the manage used in the org chart setting and also if you would like users to be put in extranets.