If you tried using WHM's Transfer Tool on very large sites, you've probably got a timeout error.
To fix this, we'll need to do this through SSH (via root) what the Transfer Tools wasn't able to do itself.
The Transfer Tool will create a /scripts directory--with all required scripts--at the base of your server, which we will use to create WHM/cPanel compatible backups.
The name of the script will look like the following: /scripts/pkgacct.YOUR_CPANEL_SERVER_NAME
Type the following to get the exact name:
ls -la /scripts/
Next, go into your /home directory to get a listing of the account names.
cd /home ls -la
Once you see the account you want to make a WHM/cPanel compatible backup, we now can run the Transfer Tool script to make our cPanel compatible backup.
Once done, you'll have your cPanel compatible backup. Now make sure it's readable by everyone, since you're going to be downloading to your cPanel server.
chmod 777 /home/cpmove-ACCOUNT_NAME.tar.gz
From here, move it to a public_html location--preferably someplace secret.
mv /home/cpmove-ACCOUNT_NAME.tar.gz /home/SOMEOTHERACCOUNT/public_html/SECRET_DIRECTORY
Now SSH into your cPanel server and download the backup.
cd /home wget http://CPANELSITE.com/SECRET_DIRECTORY/cpmove-ACCOUNT_NAME.tar.gz
Once done, go into WHM --> Backup --> Restore a Full Backup/cpmove File. Select "Restore with Username". Type in the backed up ACCOUNT_NAME under Username for the account that you wish to restore.
And.... we're done.