Iis – How to kill a particular in memory session in IIS console

You know that out of the box, IIS (6.0) restarts all app pools every 29 hours? So, unless you've changed the settings, it's restarting itself almost daily anyway. When it dies, if it does it every few weeks/months, it's not because it's been up too long since the last restart.

Under what criteria would you have for triggering the app pool restart? Do you only know when the users start calling? Are there any event viewer entries that you can trigger off of? You can also tell IIS to restart a given app pool after a certain amount of memory consumed or number of requests done - maybe you can hook up some monitoring and figure out a threshold that means you need to do this, and then either do it through IIS, or if the condition is more complex, then instrument an automated way to call iisapp.vbs /a NamedAppPool /r

/Edit - re-read the OP, and you're saying that the application pool actually stops, on its own, and won't restart without the user manually recycling it? There should definitely be an application or system event viewer entry for that - you may have to turn up your IIS app-pool alerting to see it or it might already be there.

Judging by your question it seems that you have a central session state server (DB?) that keeps track of the session data?

You must also synchronize the machine key which is used for encryption for any forms authentication etc to work. This might also affect the session identification, I'm not sure.

Configuring Machine Keys in IIS 7

Furthermore, you should make use of the shared configuration between the machines, it might itself fix the issue with different machine keys.

IIS Configuration Synchronization for Web Server Farm?

EDIT: When you changed the site ID, did you try to restart IIS manager to see if the webroot had changed? Maybe the configuration is connected to the ID meaning that a change in ID also modifies stuff like the document root etc