The subject disclosure is directed towards changing a file from a fully deduplicated state to a partially deduplicated state in which some of the file data is deduplicated in a chunk store, and some is recalled into the file, that is, in the file's storage volume. A partial recall mechanism such as in a file system filter tracks (e.g., via a bitmap in a file reparse point) whether file data is maintained in the chunk store or has been recalled to the file. Data is recalled from the chunk store as needed, and committed (e.g., flushed) to the file. Also described is efficiently returning the file to a fully deduplicated state by using the tracking information to determine which parts of the file are already deduplicated into the chunk store so as to avoid their further deduplication processing.