Hi ,
We have this problem before and we found that the issue resolve from our server is that it is missing the subdomain entry in the httpd.conf file.
We added back the entry and the subdomain works fine again.
<VirtualHost serverIP>
ServerAlias subdomain.domain.com
ServerAdmin
webmaster@subdomain.domain.com
DocumentRoot /home/Username/public_html/subdomain
BytesLog domlogs/subdomain.domain.com-bytes_log
ServerName subdomain.domain.com
ScriptAlias /cgi-bin/ /home/Username/public_html/subdomain/cgi-bin/
CustomLog domlogs/subdomain.domain.com combined
</VirtualHost>
Hope this help.
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