Ever since after the up gradation of WHM to higher versions, there can be many issues of lost or unlisted addon/parked domains in Cpanel. The domains will be present in /etc/userdomains, but still fails to be seen in the email account creation tab in Cpanel. This is mainly beacuse of the XDNS entries in /var/cpanel/users/<cpanel_username>
If your required domains are marked as XDNS, then rename XDNS to DNS of all the required domain entries. After this you have to run the following script to update the userdomains
After running this script, the domains will be found available for new account creation. Also the previously created accounts will be restored back.