Yes, in v2, if the web.xml is changed, a redeploy (or reload) is needed.
Just deleting the web.xml from the generated/xml directory would cause problem. That web.xml has the combined meta-data information from the original web.xml and also annotations. Deleteing it would force the web.xml to be loaded from the original user directory, and therefore possible loss of the annotation information.
[Message sent by forum member 'hzhang_jn' (hzhang_jn)]
http://forums.java.net/jive/thread.jspa?messageID=284689