Check is there any main domain is created with the same name

Else follow the steps below.
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/scripts/killdns <domain>

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Also check these locations

/var/cpanel/users/username file
/var/cpanel/userdata/username/main file
/var/cpanel/userdata/username/sub.domain1.com file
grep -r <domain> /var/cpanel/users
/scripts/updateuserdomains

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grep -r <domain> /var/cpanel/userdata
/scripts/rebuildhttpconf