Hi,
If you want to delete the _entire_ account for a user (including the INBOX and all subfolders), you can do this by running the command:
mboxutil -d user/<uid>/INBOX
If you have deleted the .msg files for the user off disk manually, you will need to run:
recontruct -r user/<uid>
You don't need to delete the store.idx file.
Regards,
Shane.