[Mosu]

Think of things like aspect ratio handling (the bitstream AR might be removed/added/changed to match the container AR); dummy frames in MPEG4 part2 that are removed completely.

ID3 tags are stripped from audio files.

For text subtitle formats some reformatting is done -- e.g. attachments like fonts and images are removed from SSA/ASS bitstreams and kept as attachments in the Matroska files. VobSub subtitle files are stripped of the surrounding MPEG program stream container, and even the SPU packets themselves are sometimes fixed because length fields are bad due to buggy authoring software.

You see, there are numerous cases in which the bitstreams get modified themselves, not just the meta information (timecodes etc).

However, all of those changes to not degrade the quality of the content. Like I said, audio/video is not re-encoded in the process.