A system and method for inserting checkpoints into a data stream and for restarting an asynchronous transmission of a data stream from a source file system to a destination file system is provided. The data stream can be a set of changes between a base snapshot and incremental snapshot of the source file system for update of a replicated file system on the destination. State information relating to the progress of the source in processing and transmitting the data stream is stored at regular intervals, and a checkpoint number associated with each stored segment of the state information is inserted into the data stream. The destination tracks the fall commitment of each segment of the data stream to persistent storage on the replicated file system. If an error or communication loss requires the data transfer to be restarted, the destination sends the checkpoint number associated with the last fully committed segment of the data stream. The source reinitializes its data gathering processes using the state information associated with the particular checkpoint number. The changes sent from the source file system to the destination file system relate to a sub-organization of a volume on the source such as a qtree, identified by a qtree identifier (ID) in the associated inodes and data stream.