I recently had a 5.0.9 Zimbra mailbox with inconsistencies between metadata (MySQL DB) and blob store (/opt/zimbra/store/...) in which the store was missing blob data referenced in the database.
Once I parsed the zmblobchk report data to retrieve information for the mailbox I wanted to fix, I wanted an efficient way to remove the blob item references from the database.
All commands run as zimbra user.
A snip from zmblobchk's mb8blobcheck.rpt file:
* MailboxGroup=8, mailbox=8, item=397: file not found: 397-2020.msg (delete associated metadata)