Product:
Cognos Controller 10.3.1
Microsoft Windows 2012 R2 server

Problem:
Cognos Controller Users are disconnected from Server, and have to start there Cognos Controller client again and login.

Suggested Solution:
Change the Recycle from default 29 hours to a specific time at night, when few users are using Cognos Controller.

Login to the Cognos Controller Server.
Open Internet Information Services (IIS) Manager
Click on Applications Pools
Click on DefaultAppPool or the one created for Controller.
On the right side click on Recycle…

Unmark the default of 1740 minutes intervals.
Mark Specific times
Enter 3:00 AM

Click Next

Click Finish.

Let the user test Cognos Controller more than a day before you define if this solve your issue.

More information:
https://www-01.ibm.com/support/docview.wss?uid=swg21990348
https://www-01.ibm.com/support/docview.wss?uid=swg21969315