The "whostmgr2" is the binary that contains the necessary code for applying changes made to cpanel.config.
Are you trying to update cpanel config and cpupdate files manually ?
When we make changes in /var/cpanel/cpanel.config, /etc/cpupdate.conf etc, we execute "whostmgr2" tcommand to save the tweak settings.
eg:- /usr/local/cpanel/whostmgr/bin/whostmgr2 --updatetweaksettings