Why are all configs lost when starting Jenkins as another user on Tomcat?
This is probably an issue with where Jenkins expects to find its configuration files. If you have the environment variable JENKINS_HOME defined, it will look in $JENKINS_HOME, otherwise it will use the subdirectory .jenkins in the home directory of the user running the Tomcat server.
In your case, I'm guessing that the Jenkins configuration files are in .jenkins under the home directory of the user that you first started Jenkins with.
See the Jenkins administration documentation for more details.