On a Cpanel Server, Clicking on Manage SSL sites

I get error

A fatal error or timeout occurred while processing this directive

When checking the Cpanel error logs at

tail -f /usr/local/cpanel/logs/error_log 

Got following error

[2017-07-29 09:57:24 +0000] die [Internal Death while parsing ./frontend/paper_lantern/ssl/install.html.tt 15562] Template::Exception:
    [TYPE]=[undef]
    [INFO]=[SSL::installed_hosts() failed: Unrecognized vhost: “second-addon-domain.com.customer-main-domain.com” at /usr/local/cpanel/Cpanel/Config/WebVhosts.pm line 292.

]
    [TEXT]=[]
 at cpanel.pl line 1267.
    cpanel::cpanel::cptt_exectag("/usr/local/cpanel/base/frontend/paper_lantern/ssl/install.htm"..., 1) called at cpanel.pl line 5226
    cpanel::cpanel::run_standard_mode() called at cpanel.pl line 874
    cpanel::cpanel::script("cpanel::cpanel", "./frontend/paper_lantern/ssl/install.html.tt") called at cpanel.pl line 304

Reason for error

Customer added an addon domain second-addon-domain.com, for some reason apache virtual host for this site is missing. This domain was not listed in cpanel to remove it using cpanel.

Solution

You need to mannually remove all entry for this domain from following locations

/var/cpanel/users/$username
/var/cpanel/userdata/$username/ 

Example

root@server48 [/var/cpanel/users]# grep  second-addon-domain /var/cpanel/users/*
/var/cpanel/users/salbendo:XDNS1=second-addon-domain.com
/var/cpanel/users/salbendo:XDNS2=second-addon-domain.customer-main-domain.com
root@server48 [/var/cpanel/users]# 

Removed the 2 entry from the file /var/cpanel/users/salbendo

Now in users data folder, check for the doamin

root@server48 [/var/cpanel/users]# cd /var/cpanel/userdata/salbendo/
root@server48 [/var/cpanel/userdata/salbendo]# ls -l | grep second-addon-domain.com
-rw-r--r--   1 root root       719 Mar 23 06:27 second-addon-domain.com.customer-main-domain.com_SSL
-rw-r--r--   1 root root       764 Mar 23 06:27 second-addon-domain.com.customer-main-domain.com_SSL.cache
root@server48 [/var/cpanel/userdata/salbendo]# rm -f second-addon-domain.com.customer-main-domain.com_SSL 
root@server48 [/var/cpanel/userdata/salbendo]# rm -f second-addon-domain.com.customer-main-domain.com_SSL.cache