A system and method for updating a replicated destination file system snapshot with changes in a source file system snapshot, facilitates construction of a new directory tree on the destination from source update information using a temporary or "purgatory" directory that allows any modified and deleted files on the destination active file system to be associated with (e.g. moved to) the purgatory directory if and until they are reused. In addition, an inode map is established on the destination that maps source inode numbers to destination inode numbers so as to facilitate building of the destination tree using inode/generation number tuples. The inode map allows resynchronization of the source file system to the destination. The inode map also allows association of two or more destination snapshots to each other based upon their respective maps with the source.