The web.xml needs to be updated only if you have made any modifications to it.
An upgrade doesn't carry forward manual modifications made by end user. THe software will update the web application to a vanilla/default state.
So I'd recommend that you start by redeploying the web applications first. Worry about modifications later (you may not even have to, if your webapps were not customized in anyway).
Use wdeploy to redeploy these web applications. Once you're done with that, test whether CMC / Launchpad works correctly.
-Sid