DNS and userdomains confision cause this problem you can solve this problem by follow this way:
Code:
/scripts/updateuserdomains
This command will result some dns errors, and it will say someting like this yourdomain.com dns already in another username file.
Then what you do open the file
Code:
pico /var/cpanel/users/username
find the problem domain or dns entry and remove it save the file. Thats it then try use /scripts/updateuserdomains again lets see if any dns error return again about your lost domain do same actions again. If not you can see your domain on the whm list now.
If you cant solve this problem contact me on msn i will help more. My msn below in my sig.