1. In a computing environment, a method performed at least in part on at least one processor, comprising, re-optimizing a partially deduplicated file having at least one undeduplicated portion-into a fully deduplicated file, in which the partially deduplicated file further has at least one deduplicated portion that is maintained in a chunk store and is referenced by metadata associated with the partially deduplicated file, the re-optimizing including processing each undeduplicated portion of the file to determine at least one chunk, committing the at least one chunk to a chunk store, and modifying metadata associated with the file to include a reference to each chunk that is committed to the chunk store.