A system is provided for backing up and synchronizing data stored within a set of programmers used for programming implantable cardiac stimulation devices such as pacemakers or implantable cardioverter defibrillators (ICDs). The data from the programmers that is backed up and synchronized includes programmer software, set up and configuration data, programming parameters, patient personal data, implantable device diagnostic data, and patient diagnostic data received from implanted devices. The implanted devices are classified into one or more groups and the programmer backup system merges and synchronizes data received from all programmers within a particular group. In other words, the backup system operates to ensure that each programmer within a particular group shares the same set up and configuration data, programmer software, patient contact data, and device diagnostic information. Programmers within different groups may have different data stored therein, particularly different set up and configuration data, patient data and the like. The merging and synchronization of data may depend upon the particular type of data. For example, all devices connected to the backup system may be synchronized to have the same programmer software, whereas only programmers within a particular group may be synchronized to have the same set up and configuration data, patient data, and the like.