The network hierarchy in Binary MLM Pro and Binary MLM eCommerce is stored in the DB. The network genealogy is stored in custom tables outside of standard WordPress tables.
For this reason we do not have a delete / move user functionality in our plugin as that disturbs the entire genealogy. However, the delete user functionality still exists in default WP under Users -> All Users. If you delete users from that interface, they are only deleted from the standard WP Tables and NOT from the MLM tables. This will result in inconsistencies with your DB as the users would continue on the show on the genealogy but they are actually deleted from WP. They will not be able to login as their account has been deleted.
Please do not delete users from the All Users page in WP Admin as that would break the entire genealogy and MLM functions. If this has already been done then the only way to fix the issue is by manually fixing the DB via PhpMyAdmin. As of now we have provided the Reset MLM data under the settings option of our Binary Plugins which removes ALL the users and settings from both WP and MLM Tables.