A customer with a large number of users in LDAP in 3.4.x or below would need to set up 3.5+ without migrating the atlassian-user.xml file (as automatic migration for large LDAP instances is not supported), so that no LDAP directory is set up in 3.5+. This involves adding the LDAP directory again manually, but all group memberships between LDAP users and local groups or LDAP groups and local users are lost. Confluence doesn't currently support an easy migration of this configuration.
A manual migration process needs to be put in place that allows such users to migrate their memberships.
Follow the "Resolution" steps in the LDAP synchronisation process takes too long if number of users or groups is large KB article.