Could it be that for some reason the XAP in your web project is not getting updated? If you have not already tried this, delete the XAP file in the client bin of your web project. Now when you rebuild your application, the xap should reappear. If it doesn't then you should check if the link between your web project and your SL project is broken. You can do this by going to the Property Pages of your web project and clicking on the Silverlight tab.
Jim (http://jimmangaly.blogspot.com/)
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