Should really be in the Intranet list but I don't think that matters.
First off stop Tomcat, navigate to the Tomcat55\work\Catalina\localhost and delete all the content there. Restart Tomcat and go and get a coffee - all the web apps will be redeployed from the webapps directory. It can take a while depending on the server - it's all disk activity really.
Then try it.
If that doesn't work. Stop Tomcat and delete the working content again. Then undeploy and redeploy all the war files using wdeploy in the deployment directory- in the command prompt navigate to the deployment directory and wdeploy tomcat55 undeployall will remove everything; wdeploy tomcat55 deployall will redeploy it (go to lunch as this will take much longer) and then restart Tomcat.
Bear in mind that this will deploy whatever is in the source .war files - i.e. any manual changes or customisation you have made in the Tomcat dirs you will have to re-apply - anyway you should be doing this in the source war files in BusinessObjects Enterprise 12.0\java\applications.
