H.264/MPEG-4 AVC standard appears highly competitive due to its high efficiency, flexibility and error resilience. In order to maintain universal multimedia access, statistical multiplexing, or adaptive video content delivery, etc., it induces an immense demand for converting a large volume of existing multimedia content from other formats into the H.264/AVC format and vice versa. In this work, we study the remultiplexing and resynchronization issue within system coding after transcoding, aiming to sustain the management and time information destroyed in transcoding and enable synchronized decoding of decoder buffers over a wide range of retrieval or receipt conditions. Given the common intention of multiplexing and synchronization mechanism in system coding of different standards, this paper takes the most widely used MPEG-2 transport stream (TS) as an example, and presents a software system and the key technologies to solve the time stamp mapping and relevant buffer management. The solution reuses previous information contained in the input streams to remultiplex and resynchronize the output information with the regulatory coding and composition structure. Experimental results showed that our solutions efficiently preserve the performance in multimedia presentation.