restart tomcat after running the reconcile script.
zmpurgemessages is just a wrapper around a soap call, so using the 4.0 version in 3.1.4 won't get you 4.0 behaviour.
Also - all this crap is fixed in 4.0, anyway.
Tomcat restart helped. There was some timeout error when I ran zmpurgemessages again, but I guess it was because lot of messages (tens of thousands) were being deleted. After second run it looks that messages have been purged successfully.
Thanks for your excellent support!
after running the zmreconcilembdb and restarting tomcat
I get an error saying "Received SOAP fault: authentication failed for zimbra" when trying to run zmpurgemessages