If you are suffering from timeouts and the application expects the TCP session to remain open then configure a TCP profile with the appropriate timeout. Given this is a web application I am surprised this is needed. If you are able to watch a tcpdump while its running this will show you what is happening.
Essentially a web application usually will send additional http requests to get updates so TCP connection timeout is not usually an issue. If however you are using cookie pesistence, just make sure the clientside support cookies.