If you create a new web application project with existing sources, then the existing web.xml file is overwritten with a new one.
Steps to reproduce:
1. Create a web application without using Eclipse. It is sufficient for this bug to have a directory called WEB-INF and a web.xml file in it.
2. Create a new project by going to File, New Project and selecting Web Application under the MyEclipse, Java Enterprise Projects folder.
3. Ensure the project is located in the same location as your existing web application.
Like a Java Project created in Eclipse, I expect it to determine that I already have sources and I want these used in my new project. That means, I expect my existing web.xml to be used. However it is overwritten with a default web.xml file.