It appears that all manual workspaces have their root directories reset with each sync. I have a Pipeline job read from a source controlled Jenkinsfile that references a global library resulting in 3 different clients. In each of them I am seeing the client root continually reset.

Pipeline job client: jenkins-master-1.0.0-AppName
1. Client root is set first to the proper directory = $JENKINS_HOME/workspace/JobName
2. Client root is finally set to just $JENKINS_HOME

The same behavior is exhibited in:
Pipeline Jenkinsfile client: jenkins-master-1.0.0-AppName-Jenkinsfile
Global library client: jenkins-master-1.0.0-Library

This has resulted in hundreds or thousands of unneeded specs in the spec depot and also restricts the ability to run manual p4 commands using the “sh” build step