So I ran the trace in debug and got following trace:
 - [Thread: qtp0-4]18:07:56.774 DEBUG
[org.apache.shiro.session.mgt.AbstractSessionManager]  Stopping session with
id [1276812180204]

<!--- This is line is from my update(Session session) code --->
 - [Thread: qtp0-4]18:07:56.774 INFO  [mypkg.SessionDAO]  >>> updateSession
id: 1276812180204
<!--- This is line is from my update(Session session) code --->

 - [Thread: qtp0-4]18:07:56.899 DEBUG
[org.apache.shiro.web.attr.CookieAttribute]  Not value found in request
Cookies under cookie name [JSESSIONID]
 - [Thread: qtp0-4]18:07:56.899 DEBUG
[org.apache.shiro.web.attr.CookieAttribute]  Not value found in request
Cookies under cookie name [rememberMe]
 - [Thread: qtp0-12]18:07:56.899 DEBUG
[org.apache.shiro.web.attr.CookieAttribute]  Not value found in request
Cookies under cookie name [JSESSIONID]
 - [Thread: qtp0-12]18:07:56.899 DEBUG
[org.apache.shiro.session.mgt.DefaultSessionManager]  Creating new EIS
record for new session instance [ sessio

So I do see calls being made to AbstractSessionManager
(AbstractNativeSessionManager) and my update code but it never calls the
delete(). And but ofcourse, it doesn't delete the record from DB backend.

 
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