Have you tried to disable "Incremental Synchronisation" by un-ticking this option from the directory configuration. If that doesn't work, could you double check how your LDAP admin removed the user from your LDAP server, if it only disabling it, Confluence won't be able to understand that and will still include the users (unable to authenticate though).
You might want to exclude the user from your search filter to workaround this issue. Or you can also, ensure he don't have "Can-Use" permission in Confluence (removing his group membership and ensuring his name is not in Global Permission page), so the user still available in Confluence (history intact) but he won't be counted as licensed user.
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