I have a web application that has a Spring Integration logic running with it in a separated thread. The problem is that at some point my Spring Integration logic tries to us
You can only use request (and session) -scoped beans on the web container thread on which the request is running.
I presume that thread is waiting for an async reply from your SI flow?
If so, you can bind the request-scoped bean to the message, perhaps in a header, or somewhere in the payload.