Metadata of each file of a group of files of a storage and chunk file metadata are analyzed to identify one or more file segment data chunks that are not referenced by the group of files of the storage. Fragmented chunk files to be combined together are identified based at least in part on the one or more identified file segment data chunks. The chunk file metadata is updated with an update that concurrently reflects the removal of at least a portion of the one or more file segment data chunks that are not referenced by the group of files and the combination of the identified fragmented chunk files.