In Aras Innovator, every files normally link to particular Item by Property or Relationship. When deleting Item, relevant physical file will not be removed. Obviously, these orphaned files will increase with time, of course it could be treated as a special way to protect physical files from accidentally deletion. In order to keep vault data consistent with database records, variable "Force.Delete.Orphaned.Files" can control if system need to handle physical file or not. But this variable does not exist in default, you need to create it by yourself. If set to 1, orphaned files will be removed together once relevant Item is deleted.
Programming notes from a non-expert guy who keeps learning in various applications.