Well, first of all to ascertain the full impact you could run
Code:
su - zimbra
zmblobchk
It would also be helpful if you would update your profile with the following output so we know which version of ZCS you are running
Code:
su - zimbra
zmcontrol -v
Well, there is probably a easier way of doing what I am going to describe but here goes anyway
Code:
su - zimbra
zmvolume -l * this will list all your volumes so you can see which is your HSM
mysql
use mboxgroup1;
select * from mail_item where volume_id = '3' * obviously change the volume_id to be your HSM one.
You could then delete all the mail items that are in your HSM but do not have any data files. You will need to do this for all the 10 mboxgroups and then re-index once completed. Alternatively, you may just be able to remove the HSM store and all the referencial data will be updated accordingly.
NO warranty comes with any of this as I personally keep good backups 