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Action "Delete All Contexts" should delete tempDirs.properties file in userdir/system/tomcat directory. This is probably the best way how to clean this file.
File tempDirs.properties is removed in DeleteAllContextsAction.class - performAction() method Changed file : org.netbeans.modules.web.tomcat.DeleteAllContextsAction
It is not clear that the behavior should be what this report describes, reopening.
The tempDirs.properties file should be synchronized with the server.xml file, but the mechanism needs to be different than what is described in the summary. The synchronization should take place on every execution/deployment/debugging when the server is restarted.