If your Tomcat application has a docbase which is a network place (being it a Windows share or a NFS Linux share) and temporarily the connection between the two machines is lost, chances are that the context.xml of your app as it is deployed in \conf\Catalina\localhost will be automatically removed.
In order to avoid this, edit your server.xml file and set autoDeploy="false" in the Host tag.
See https://issues.apache.org/bugzilla/show_bug.cgi?id=40050
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