I've got an additional information from my colleague. He tried as a work-around to split the web application. Hence he deployed two web applications, each containing just one of the two parts from the original web.xml. So, the backup plan does not work and it is definitely a problem.
There is some undesired sharing across the contexts. The important information here might be that our web server is Jetty embedded in Equinox OSGi container with classical deployment model (i.e. not WABs, just common web applications), but I guess it could happen in a different environment too.
