Hivos, I think you're answering in the context of NETWORK edition. Strafford has FOSS according to his profile.
Strafford, I assume you are downing Zimbra before doing your nightly backup. That's a baseline absolute "must" unless you have implemented something exotic.
However if you do something like this, you may be able to forego downing the server. Or at least, the concept could be used to provide backups of individual folders, as a supplement to making a backup of all of ZCS. The basic idea is to script using the built-in account-level Export feature.
These will help you get started with what you'd need to do: ZCS 6.0:Zimbra REST API Reference:Export Mailbox - Zimbra :: Wiki
ZCS 6.0:Zimbra REST API Reference - Zimbra :: Wiki
Basically, I think you could use
to backup each mailbox. You could use tgz instead of zip if you like. Then you use
zmmailbox -z -m <mailbox name> getRestURL "?fmt=zip" > <filename.zip>
to restore a given account. Probably you'll want to create a dummy account to restore to, and then share whatever folder has the data you want to recover. Alternatively you could try doing folder-specific restores, or you could do folder-by folder backups for each account.
zmmailbox -z -m <mailbox name> postRestURL "?fmt=zip" <filename.zip>
I can't promise this will be economical either in time or disk space.