The tomcat 6.0 document at http://tomcat.apache.org/tomcat-6.0-doc/config/context.html says:
Only if a context file does not exist for the application in
If you want to avoid overwriting of 'context.xml', you could go to Tomcat Manager url and then uninstall the previous app and install the new war/ear. This way you have more control on the installation process.