This is going to be a TEDIOUS & LONG processs as far as I know.
For a start, you can try adding the missing main domain back by editing /var/cpanel/users/YSERNAME
If that fails to you cannot remember the user (unlikely), then:
1. Terminate those you can see under WHM > TERMINATE MULTIPLE ACCOUNTS
2. Terminate their Zones under WHM > DELETE ZONE ENTRIES (those you cannot see)
3. EDIT as root /etc/passwd, /etc/group and remove their usernames
4. Go to /home and remove their directories with rm -rf /USERNAME
5. Go to /var/cpanel/users and DELETE their USERNAME
The above "should" make a "clean" delete of those stealth accounts, although there are other entries which in my opinion are safe to ignore.
I am sure there must be an easier way and I have yet to figure them out
