A video stream is transcoded to provide a plurality of primary profiles. Individual frames of the video stream have a Presentation Time Stamp (PTS). A PTS is used as a token to identify particular frames to be encoded as Instantaneous Decoder Refresh (IDR) frames in each profile. An IDR frame period is determined, indicative of a desired number of video frames between two IDR frames. An IDR frame is inserted into each profile every IDR frame period. The IDR frames of each profile are aligned with the same IDR frames of the other profiles. The PTS of each IDR frame in each profile is monitored. Upon determining that a PTS is out of alignment, the next PTS of the affected profile is aligned with the corresponding PTS of remaining profiles. Backup transcoders produce backup profiles that are maintained in alignment with each other and with the primary profiles.