The custom workspace of a Jenkins job cannot be removed by the CLI using update-job.
Steps to reproduce:
1. Have a job with a custom workspace.
2. Remove the custom workspace using the Jenkins java CLI (having a second job without the custom workspace and doing <cli> -get-job <second job> | <cli> update-job <job> is how we encountered this problem).
3. Note that the config.xml of the job no longer references a custom workspace.
4. Open the job in the Web GUI. Note that the custom workspace is there, and a save of the job without doing any updates will put the custom workspace configuration back into the config.xml file for the job.
Bottom line - to remove the custom workspace, one either needs to do it via the web GUI, or do a restart of the Jenkins instance after doing it via the CLI.
Side note: the " and some other characters are save differently when updating a job via the CLI vs. the Web GUI.
Example: double quotes " will be changed to '"' in config.xml through CLI method.