Running Neo4j Community 2.3.3 on Ubuntu 14.04, I recently saw a drastic 
drop in the total store size as reported in the browser monitor page. It 
went from 456GB to 120GB. Roughly at that time I was re-configuring 
keep_logical_logs, but no actual neostore.transaction.db files were deleted 
when I restarted Neo4j. 

Our use case is such that we are constantly adding new relationships and 
deleting old relationships based on age

Did this restart clean up deleted objects?

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