Steps to rebuild userdata files with a valid httpd.conf file

1. The corrupt userdata directory must be moved to a new location.

You can do this by using the mv command to move the directory and its contents to a new location.
mv /var/cpanel/userdata /var/cpanel/userdata.orig

2. A new userdata directory must be created.

To create new user data directory use mkdir command
mkdir /var/cpanel/userdata

3. To rebuild userdata files run userdata_update script

The /usr/local/cpanel/bin/userdata_update script restores userdata files for all of the accounts that are present on your server.
/usr/local/cpanel/bin/userdata_update –reset

4. To validate the userdata permissions settings run the script fix_userdata_perms

The /usr/local/cpanel/bin/fix_userdata_perms script makes certain that all of your server’s userdata files and directories are assigned the correct permissions settings.

5. To update the system’s cache run script updateuserdatacache.

The /scripts/updateuserdatacache script makes sure that the system appropriately caches all userdata files.

6. Restore Apache.

To use the rebuilt userdata files, you must rebuild Apache.

7. Apache Restart is required

Restart Apache on your server after you rebuild it.