When JIRA is using more than one User Directory, the user count can get incorrect after User Directories are removed and added a few number of times.

I'm not sure how JIRA is counting users toward the license today, but I believe the following query should return the most correct user count.

SELECT distinct u.lower_user_name
FROM cwd_user u
JOIN cwd_membership m
ON u.id = m.child_id
AND u.directory_id = m.directory_id
JOIN schemepermissions sp
ON LOWER(m.parent_name) = LOWER(sp.perm_parameter)
JOIN cwd_directory d
ON m.directory_id = d.id
WHERE sp.permission IN ('0','1','44') AND d.active = '1' and u.active = '1';

The query may need some changing considering nested groups.