Just a short update, I've tested out affa on a dummy server and it does exactly what I'm looking for. This is a pretty amazing tool.
Before for backing up mail I've just been rsyncing the mail to a remote machine, I think I'm going to be using affa from here on in.
I'll be running it on the live server over the weekend, I'll post an update with how long it takes to get all 60GBs of mail down when I'm done.
Conor