Systems and methods are disclosed for synchronizing one or more user data sets on one or more client devices of a user, using a synchronization system. Each client device can have two independent and asynchronously-operating synchronization engines. The synchronization system can include a synchronization system manager that can resolve conflicts in data that arise from different versions of software being used generate a data set. Each client can maintain two separate databases: a first database that can contain a snapshot of the state of the user data sets across client devices, as known to the synchronization system. The second database can contain a snapshot of the local file system and information about the state of synchronization of the local file system with the synchronization system.