OS X Server Updates overwrite tomcat configuration files

I have a tomcat installation running on OS X Server. Whenever I perform a mac software/security update, my /Library/Tomcat/bin/catalina.sh and /Library/Tomcat/conf/server.xml files are both overwritten and restored to the default settings.
This is a huge problem because I have tomcat tuned to run with 4GB of memory and in 64 bit mode. I also have the server.xml tuned for efficient connector pool usage, max connections, etc.
All of my setting are wiped out by the OS update crippling my web apps with the default 64M of memory and such.
Any advice would be much appreciated.
Thanks In Advance.

The Question is how to get Apple to fix SSLPassPhraseDialog exec:/etc/httpd/getsslpassphrase
Any ideas ?
File a bug report with Apple via its Bug Reporter system. Go to https://connect.apple.com/MemberSite and join the Apple Developer Connection (ADC)—it's free and available for all Mac users and gets you a look at some development software. Then, go to https://bugreport.apple.com/
click on the Login to the Apple BugReporter link (using your Apple ID username and password), and file your bug report/enhancement request. The nice thing with this procedure is that you get a response and a follow-up number; thus, starting a dialog with engineering.
BTW, you'd probably get more sympathy posting to the server forums at http://discussions.apple.com/category.jspa?categoryID=96

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