A config backup is only a couple of MB. It should not overwrite your data at all. Was it a recent backup? Could it have got rid of storage mounts made after the backup or made manually? Do you have a more recent config backup you could restore over the top?

Well exactly - 3.4MB to be precise. It was the latest config backup that we had, but it seems that all data on the server (including /var/flexhare) before the backup date was removed. It didn't remove any storage mounts, but it took out a significant amount of data. A warning that this was going to happen would have been nice!

Now we've restored the config backup, it looks like we need to reconfigure the network too - already way out of my depth on this!

This all sounds wrong. The config backup does not fully backup the network settings as it is typically used when people need to transfer settings to another server like I did when setting up a 7.x server form a 6x live one. You don't want to copy over the network settings as all the interfaces will probably be different in the new server. It is also dangerous to restore firewall rules to a different server as hardcoded interfaces can make the firewall panic.

I am still thinking there is an issue with storage mounts if you think everything under /var/flexshare has gone. What is the contents of /etc/fstab?

This is not a new server, it's an existing server that was having some problems, and a config backup was restored to try and fix the problems. It is now working as a firewall. The only data lost is the recent contents of /var/flexshare since the date of the backup that was restored.
The contents of /etc/fstab is:

#
# /etc/fstab
# Created by anaconda on Wed Jan 15 11:43:51 2014
#
# Accessible filesystems, by reference, are maintained under '/dev/disk'
# See man pages fstab(5), findfs(8), mount(8) and/or blkid(8) for more info
#
UUID=99b6156e-3046-4a82-b6de-631d6f19de56 / ext4 defaults 1 1
UUID=50ac0d4d-ad35-4577-970c-9cf1c56a7171 /boot ext4 defaults 1 2
UUID=a6e4383b-2803-4183-ad59-f281ce0b2738 swap swap defaults 0 0
UUID=b23a06af-0eed-4acd-aff3-0c86a2c9cad1 swap swap defaults 0 0
tmpfs /dev/shm tmpfs defaults 0 0
devpts /dev/pts devpts gid=5,mode=620 0 0
sysfs /sys sysfs defaults 0 0
proc /proc proc defaults 0 0
/dev/sdc1 /backups ntfs defaults 0 0
/dev/sdd1 /var/flexshare/shares/archive ntfs defaults 0 0

The issue now seems to be that workstations logged in to the network prior to the backup being done and still logged in now can see the server, but all other workstations cannot log in to the domain or cannot see the server despite being on the network, indicating its a network config issue with Samba and Windows 7.
We've tried editing the smb.conf file as suggested elsewhere, including: http://www.liberiangeek.net/2012/03/how-to-fix-failed-to-retrieve-share-list-from-server-in-ubuntu-12-04-11-10-when-file-sharing-with-windows/ but no change.

We've also done:
wbinfo –t which showed that trust is working
net getdomainsid which showed at the SIDs matched
slapcat –n3 |grep sambaSID which showed no long SIDs mismatched
net join –U winadmin and the server joined the domain fine.