How top prevent Idea wiping out my directories..

I have an existing webapp (which is deployed through a war file), lest say into:

webapps/Existing/

Now I made a new web module, and I'd like to deploy some jsp's (into webapps/Existing/new/ )and some classes into webapps/Existing/WEB-INF/lib/classes

However, Idea wipes all existing directories empty , even jar files from within lib directory.

Is there a workaround/setup I could use for these situation(Note: i don't have sources of existing app)

Thanks in advance...