ftp use the user home direct from the /etc/passwd, looks like the script got terminated before cpanel change the httpd.conf to fix it
login to the sheel and use the usermod command
Code:
usermod -d /home/username username
which will change home directory for that users to whatever you give beside -d
Reference : man usermod
The usermod command modifies the system account files to reflect the changes that are specified on the command line. The options which apply to
d home_dir
The user’s new login directory. If the -m option is given the contents of the current home directory will be moved to the new home direc-
tory, which is created if it does not already exist.