This has become a common problem with customers who have web app context configured in their server.xml.
What is happening is people are deleting their war files before uploading a new one. Unfortunately, this also removes the deployed web app directory, and if you have a context set up for that web app, tomcat is not going to find it and fail.
The best thing to do is to upload the new war file without first removing the old one. If the name is the same, it will simply overwrite the old war and tomcat will redeploy the war replacing the old web app directory.
It is also a good idea to clear your cache in Tomcat Control.
The lesser alternative is to first comment out the context in your server.xml before removing your web app.