1. A method for performing two-way orphan reconciliation in a Hierarchical Storage Management (HSM) controlled storage environment, comprising: operating an HSM application suite on a distributed storage system, the distributed storage system comprising a file system and a storage repository server connected over a network; migrating a plurality of data files with the HSM application suite from the file system to the storage repository server; performing a file indexing process with the HSM application suite to generate a unique migrated file identifier for each of the plurality of data files upon migration, wherein the unique migrated file identifier is stored in a stub file on the file system and in the migrated data file on the storage repository server; populating a server object queue with a list of the migrated data files stored on the storage repository server, the server object queue ordered by the unique migrated file identifier of the migrated data files; populating a file system queue with a list of the stub files stored on the file system, the file system queue ordered by the unique migrated file identifier of the stub files; and identifying file system orphans and server object orphans by executing a single-pass orphan identification matching process upon the server object queue and the file system queue that compares the unique migrated file identifier of server object queue elements with the unique migrated file identifier of file system queue elements.