1. Why are they changing - I would guess that someone is using csv to upload users into courses and is not adding the auth column with ldap filled for each user.
2. Couple of ways - quickest would be to run a script on the database that updates all users with an id greater than 2 (this then excludes the guest and admin users) and with manual authentication to ldap authentication. You will need a little mysql knowledge and access to the database through Adminer or PHPMyAdmin.
3. If you only have access to the web interface, use the filter feature to find all your manual authentication users and download them to a csv file. Then take this file, change manual to ldap, and use it to upload the users back in using user import. You can delete a lot of the columns out - you basically just need username, email and auth columns. Make sure you select the option to update existing users and that should take care of it.