In one of my recent projects we were using Business Monitor and the embedded Cognos BI. During the implementation of the automated installation and configuration scripts it became apparent that not everything was scriptable, as I would’ve expected from my past experience with IBM products.
Configuration of certain Cognos parameters, such as the query size JVM parameters, initial heap size, and maximum heap size, is currently only possible through the interactive GUI web interface, but not through a scripting or API interface.
You will find that the parameters are stored in the Cognos Content Store database:
As of now there is no supported way of changing these parameters in an automated way and IBM rejected the Request for Enhancement 60988.
If you need to be able to script this, please make sure to vote for the RFE and in case you add this functionality yourself, consider publishing it and linking to your code from a comment on the RFE so everyone interested can get a notification.