Hi,
Good question - but it's not a problem. The DMS does hold a copy of the firmware, but it is only updated in the Phatbox when there is a file called "forceupdate" present. The act of re-programming the firmware causes the software in the box to delete this file, so it is a one-hit operation. Thereafter, the software only accesses the data (database and music) on the DMS, so you should be able to play the same DMS in more than one vehicle.