matroska: modify chapter limits by join_diff

When adding or removing frames to avoid 1-frame seeks on chapter
boundaries, the end of the chapter needs to be pushed or pulled by the
same amount to keep the intended end frame the same.
matroska: account for missing information from short sources

If a source is shorter than the requested chapter length, account for
the time missing.
matroska: only error if at least a millisecond is missing