The answer can be found at this link, github.com/jetty/jetty.project/issues/12938.

This is what was posted in the link by joakime

"If the work directory contents do not match the WAR it's re-extracted.
If you don't want this behavior, then don't use WAR deployment, use Directory deployment.
Just unpack the WAR into a directory in ${jetty.base}/webapps/<appname>/ and use that as the main deployment. (just don't put the WAR file in ${jetty.base}/webapps/)"

Though, I would've like an option for altering the work directory in emergency scenarios.