See this ticket:
https://ortussolutions.atlassian.net/browse/COMMANDBOX-941
Basically if someone provides a custom rewrite file and they've already put it in the correct place in the server home, runwar tries to copy it on stop of itself which wipes it out.
[DEBUG] runwar.server: Copying URL rewrite file /root/serverHome/WEB-INF/urlrewrite.xml to WEB-INF: /root/serverHome/WEB-INF/urlrewrite.xml
Check the source and destination path and skip the copy if the file is already in the correct place. This was on a Docker container.