Depending on package, you will get config file erros or missing file erros.
I think there is a script on pfsense That makes a full backup.
Try to find it searching forum or pfsense file system.
EDIT:
The scripts for full backup are /etc/rc.create_full_backup and /etc/rc.restore_full_backup
Related topic
http://forum.pfsense.org/index.php/topic,44637.0.html