What is the timeout value for?

The timeout value is used for user replies so if a reply is not received within a certain time, the ability to reply and receive information expires. The timeout setting in the parent query applies to the child user reply of that parent.

This is probably best demonstrated by an example:

A query is setup such that the message delivered to the end user asks a question. The timeout setting is 300 seconds. The user replies are set to YES or NO. If the user responds with YES or NO within 300 seconds, a response is sent back to the end user. If the end user takes longer than 300 seconds to reply, the query times out, and a response is not sent.