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When the war module is registered as a default in at least one virtual server on sunappserver the deployment fails (it's not a bug in Netbeans but a feature of sunappserver). But the sunappserver (and I think it's in j2ee 1.5 specs) provides a redeploy function which would be good to utilize in Netbeans for such cases, ie as an option to use redeploy instead of deploy in server properties.
Reassigning to the sunappserv module for evaluation.
I cannot reproduce this with v2ur2 as the deployment target. here is what I did.. register a v2ur2 domain in a recently pulled trunk build (6.5)... created a web app that is targeted to deploy on the v2ur2 domain. set the context-root to be "/" deploy the app. open the browser on http://localhost:8080/ the content of the apps index.jsp page appears. create a servlet in the web app. redeploy the app. open the browser on http://localhost:8080/NewServlet the page generated by the servlet appears. Reopen this with more detailed steps on how to reproduce the problem that you are seeing...