BuddyPress.org

Hi @alice-claire,

if the member counter shows 4.000 users and your dashboard only 2.000, wp_users table should contain around 4.000 user too.

Check this table first. Search for user status 1. In case you find some, these are probably ghost accounts.
See also wp_signup. Should normally be empty if you have no pending accounts in dashboard.

Now you can install this plugin and clean your DB.