I have made some progress with this. We have four mail queues and the problem was only affecting the 2 most active. I have managed to get e-mails working again for new tickets for these queues by duplicating the existing default template group and assigning these queues to the new template group as well as the default. I also did another full restore on the default template group.
However this still hasn't resolved the issue for existing tickets in the system, only new ones added since I did this. Any ticket that was already in the database still sends out a blank e-mail if you reply to or forward it. As we are hosting Support Suite I am not sure what is under the hood. I have tried repairing the database and rebuilding the ticket index from the Admin CP but this hasn't helped. So part way there...
