If JK aborts waiting for a response, because a reply timeout fired, there is no way to stop processing on the backend. Although you free processing resources in your web server, the request will continue to run on the backend - without any way to send back a result once the reply timeout fired.
It is possible to terminate long running requests from tomcat, but this is only on the connection side. The process will continue to run within the backend application.
Ideally the application should be able to check against this and maintain/terminate these long running threads.