[czaveri]

yes, to me it does look like your nightly backup is incorrect.

You shouldn't use "cp -Rf ..."

You should be using 'rsync' instead.

Try the following in place of "cp -r /opt/zimbra /home/backup/backups":

rsync -arlHKpogDt /opt/zimbra/ /home/backup/backups/zimbra

There are also a couple of scripts floating around on the backup and recovery threads.

My 2 Cents,