1. A document management apparatus that manages a version of a binder document formed by integrating a plurality of original documents, the document management apparatus comprising a memory and a processor which functions as: a first determination unit configured to, when updating a binder document, determine whether there is a same original document as the original document included in a new version of the updated binder document, in the original documents included in a past version of the updated binder document; a storage unit configured to, when the first determination unit determines that there is the same original document in the original documents included in the binder document of the past version, store reference information regarding the same document as information corresponding to the original document included in the binder document of the new version and, when the first determination unit determines that there is not the same original document in the original documents included in the binder document of the past version, store an entity file of the original document as the information corresponding to the original document included in the binder document of the new version, wherein the reference information has a file size smaller than that of the entity file; a deletion instruction reception unit configured to receive a deletion instruction for deleting an arbitrary version of the binder document, the arbitrary version being designated as a deletion target version; a second determination unit configured to determine whether there is reference information regarding an entity file of the original document included in the binder document of the deletion target version designated by the deletion instruction, in the binder documents of versions coming after the deletion target version; a deletion unit configured to, when the second determination unit determines that there is the reference information regarding the entity file of the original document included in the binder document of the deletion target version, move the entity file to a binder document of a movement target version which is the oldest version among the versions determined to have the reference information, and when the second determination unit determines that there is no reference information regarding the entity file of the original document included in the binder document of the deletion target version, delete the entity file of the original document; an updating unit configured to update the reference information included in the binder documents of the versions coming after the movement target version such that the entity file moved to the movement target version is referred to; and a main control unit determines whether there is an unprocessed original document having an entity in the binder document of the deletion target version, and when it is determined that there is no unprocessed original document having the entity, completing the deleting of the arbitrary version of the binder document.