So far as I know the LDAP sync only keys between the LDAP directory and the user table on the username field. I am unsure why the LDAP sync would not have just attempted to update the existing user with that username.
One issue with LDAP sync is that if a user's username changes in LDAP then you must manually change the username of the same user in Moodle to match that change, otherwise the LDAP sync would create another user. Otherwise you end up with duplicate users in Moodle. This is not exactly your situation but I'm trying to describe some behavior.
I wonder if there is some issue or bug in Moodle 29 causing this for you.
You might wish to consider if the user you deleted had any learning or activity performed, as deleting that user might have implications.
Jamie