A system, method, and processor readable medium containing code for causing a processor to synchronize a secondary database system, such as one stored on a palmtop electronic device, with a distributed database system, comprising a main database and at least one replica database. The system further comprises a modification module that contains entries for modifications that have been made to the secondary database since a previous synchronization between the secondary database and the distributed database system and a synchronization module that synchronizes the secondary database with one of the databases of the distributed database system using the modification module. Each database in the distributed database system stores an identification mapping database having an assigned version number. The system further comprises a replica identification database associated with the secondary database that contains an entry for each source database of the distributed database system, each entry comprising information regarding the last synchronization between the secondary database and the source database including the version of the identification mapping database associated with the source database when the synchronization occurred. A pruning module is provided for pruning entries from the modification module using the replication identification database.