The final fix was to get a full all accounts backup, and copy /opt/zimbra/backup to another filesystem. Then install.sh -u followed by a reinstall.
cp -pr /opt/zimbra/backup /tmp/zimbra/
3. 4. 5.
cp -pr /tmp/zimbra/backup /opt/zimbra/backup
from the Zimbra Administration console
zmrestore -a all -lb last-Full_backup (step 1.)
7. confirm everything was back.
note that I had to restore some accounts from an older backup (these were mostly accounts that had not been used at that time).
8. recheck again.
9. another Full backup
zmbackup --fullbackup --target /opt/zimbra/backup --account all