As per this link - https://www.ibm.com/developerworks/community/wikis/home?lang=en#!/wiki/Tivoli%20Endpoint%20Manager/page/Performance%20Configurations
After the tools have been run to delete out old data perform a database shrink operation on the BFEnteprise database
As per this link - https://www.ibm.com/developerworks/community/wikis/home?lang=en#!/wiki/Tivoli%20Endpoint%20Manager/page/BES%20Audit%20Trail%20Cleaner
We are no longer recommending performing a database shrink operation after running this tool to reclaim freed disk space from the database unless you are running into disk space issues.