Batch Update Permissioned Relationships
Unfortunately, there is no way to batch update relationship via the user interface b/c relationships are reciprocal. Using the Import Contacts wizard and selecting "Update" doesn't allow you to designate a relationship as permissioned either. 

If you have a programmer on hand, this type of update would be easy to do using an SQL query directly on the database:

Assumptions:


Relationship Type ID = 4 (in my environment, this is the ID for Employee/Employer)
Contact A = Individual
Contact B = Organization


Query:

UPDATE civicrm_relationship SET is_permission_a_b= 1 WHERE relationship_type_id= 4

Alternatively, if you have sufficient permissions, you could use API Explorer as documented HERE, but this should only be done by someone who has good knowledge of the CiviCRM database structure.

Good luck!