I actually don't work with Zope as much as I used to but I was going through some old notes and found this gem to backup a Zope instance's Data.fs file while the server is still running. Between the Data.fs file and the Products and Extensions folders you fundamentally have a full backup of your Zope instance.

/usr/lib/zope2.9/bin/repozo.py -BvzQ -r ./ -f /var/lib/zope2.9/instance/instance_name/var/Data.fs

Depending on where Zope is installed the repozo.py script may be in a different place. The -BvzQ is a basic options set (see the man page for details). The -r is where you are backing up to; in this example it is the current directory. And finally the -f is where the Zope instance's Data.fs is.