In a system and method for updating a remote replicated destination file system snapshot with changes in a source file system snapshot, the snapshot being associated with a qtree (or other sub-organization of the file system volume), a qtree metadata file on the destination in provided. The qtree metadata file resides, in the destination volume, and outside the qtree structure. The metadata file stores state information with respect to each qtree. This metadata file resides at a known location in the destination volume. The metadata file can include a plurality of fixed length records having respective fields for storing various information including qtree-specific information, and can be part of a hidden metadata directory.