I’ve been plagued with this annoying problem in tomcat for about a year, and it has been driving me crazy. I’ve looked through the code, joined the mailing list, etc. etc. The problem is when you have context xml files, such as /usr/local/tomcat/conf/Catalina/localhost/app.xml. Generally, you would use such files to set up JNDI data sources for database connections, but I also use them to set up configuration beans in order to keep environment-specific data outside of your application code (which I consider the whole war file to be). Anyway, tomcat seems to randomly delete those files when I change anything in the application files. I tried various configurations using war files, no war files, and war files in funny locations, and it happened to all of them.
I never did find out why it deletes the files, but I did find a solution, thanks to a user on the tomcat mailing list. All you have to do is turn off “autoDeploy” on the “Host”. Basically, you need to edit /usr/local/tomcat/conf/server.xml and change the xml element, so that it says autoDeploy=”false” instead of autoDeploy=”true”. And with that, all my problems are over.
Al's Blog 
First of all, thank you very much for this post, it was very helpful!
I just want to add, that if someone uses Tomcat but writes in Eclipse, AutoDeploy keeps becoming ‘true’ automatically due to some eclipse settings.
The process to make Tomcat stop deleting files every time it is restarted for Eclipse users is the following:
Eclipse->Window->Preferences->Servers->Launching->uncheck ‘Automatically publish when starting servers’.
I hope this helps š