You have to introduce an extra middle layers between windows and web app, this middle layer may be a Webservice which can be accessed by both other applications to communicate with each other, It can be remoting (Sorry, I have never tested calling a remote object from Web so you may have a test). In addition to the second solution if Remoting doesnot work from Web..(not recomended), to use a Windows Control in Webpage to interact with remote object and make them communicate.

But I think Webservice is quite a safe and better option here... But both applications will need to poll web service after a short interval to see if there is something new for it

Best Regards,

Rizwan