Merging of multiple encoded audio-video streams into one program with source clock frequency locked and encoder clock synchronized

A system and method for merging of multiple encoded audio and video streams into a single program in the transport stream enables playback of any audio stream with any video stream. This is accomplished by first locking the frequency of audio and video input streams for a plurality of different programs to a source clock, independently encoding each program with its own PCR and PTS into a program stream, multiplexing the program streams into a transport stream, and then synchronizing the PCR and PTS of the program streams to a declared master PCR.