Currently, if instrumentation.instanceFile.directory isn't specified, it saves the identifier based on log4j configuration. Change it to no longer use log4j configuration for this. If instrumentation.instanceFile.directory isn't specified, default to putting the file in /opt/grouper ?? e.g. /opt/grouper/instrumentation/grouperLoader_instrumentation.dat . Note that whenever a container is redeployed, a new instance would be created...
GrouperDaemonDeleteOldRecords already cleans up the old instrumentation count data. What it doesn't do is remove the old instances or instances that haven't been updated in a while. Delete old instances that haven't seen any activity in a year.