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.
STEP 1.
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/
STEP 2.
Next, go into your /home directory to get a listing of the account names.
cd /home ls -la
STEP 3.
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.
/script/pkgacct.YOUR_CPANEL_SERVER_NAME ACCOUNT_NAME
STEP 4.
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
STEP 5.
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
STEP 6.
Now SSH into your cPanel server and download the backup.
cd /home wget http://CPANELSITE.com/SECRET_DIRECTORY/cpmove-ACCOUNT_NAME.tar.gz
STEP 7.
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.