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AV-Sync issue after merging tracks with ffmpeg

AV-Sync issue occurs where:

  1. Source file has a chapter metadata
  2. Chapter #1 (closed) timestamp doesn't begin exactly on 0.0

It could be mitigated if apply AV sync +0.9, which corresponds chapter #1 (closed) metadata's offset (Further analysis is mandatory as I've only checked two samples)

Following details are based on video file which chapter #1 (closed) metadata begins with timestamp 0.911000

Original videofile

ffprobe details 
Input #0, matroska,webm, from '*****.mkv':
  Metadata:
    title           : *****
    CREATION_TIME   : 2018-11-21T22:18:26Z
    ENCODER         : Lavf57.7.2
  Duration: 00:24:15.92, start: 0.000000, bitrate: 5167 kb/s
  Chapters:
    Chapter #0:0: start 0.911000, end 139.925000
      Metadata:
        title           : Chapter 4
    Chapter #0:1: start 139.925000, end 810.929000
      Metadata:
        title           : Chapter 5
    Chapter #0:2: start 810.929000, end 1421.955000
      Metadata:
        title           : Chapter 6
  Stream #0:0: Video: hevc (Main 10), yuv420p10le(tv, bt709), 1920x1080 [SAR 1:1 DAR 16:9], 23.98 fps, 23.98 tbr, 1k tbn (default)
    Metadata:
      BPS-eng         : 1522424
      DURATION-eng    : 00:23:41.087000000
      NUMBER_OF_FRAMES-eng: 34070
      NUMBER_OF_BYTES-eng: 270437279
      _STATISTICS_WRITING_APP-eng: mkvmerge v31.0.0 ('Dolores In A Shoestand') 64-bit
      _STATISTICS_WRITING_DATE_UTC-eng: 2019-03-06 18:09:34
      _STATISTICS_TAGS-eng: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
  Stream #0:1(jpn): Audio: flac, 48000 Hz, stereo, s16 (default)
    Metadata:
      title           : Stereo
      BPS-eng         : 663155
      DURATION-eng    : 00:23:41.952000000
      NUMBER_OF_FRAMES-eng: 14812
      NUMBER_OF_BYTES-eng: 117871860
      _STATISTICS_WRITING_APP-eng: mkvmerge v31.0.0 ('Dolores In A Shoestand') 64-bit
      _STATISTICS_WRITING_DATE_UTC-eng: 2019-03-06 18:09:34
      _STATISTICS_TAGS-eng: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
  Stream #0:2(eng): Audio: flac, 48000 Hz, 5.1(side), s32 (24 bit)
    Metadata:
      title           : Surround
      BPS-eng         : 3097090
      DURATION-eng    : 00:23:41.568000000
      NUMBER_OF_FRAMES-eng: 14808
      NUMBER_OF_BYTES-eng: 550340646
      _STATISTICS_WRITING_APP-eng: mkvmerge v31.0.0 ('Dolores In A Shoestand') 64-bit
      _STATISTICS_WRITING_DATE_UTC-eng: 2019-03-06 18:09:34
      _STATISTICS_TAGS-eng: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
  Stream #0:3(eng): Subtitle: ass (default)
    Metadata:
      title           : *****
      BPS-eng         : 746
      DURATION-eng    : 00:24:10.200000000
      NUMBER_OF_FRAMES-eng: 1029
      NUMBER_OF_BYTES-eng: 135289
      _STATISTICS_WRITING_APP-eng: mkvmerge v31.0.0 ('Dolores In A Shoestand') 64-bit
      _STATISTICS_WRITING_DATE_UTC-eng: 2019-03-06 18:09:34
      _STATISTICS_TAGS-eng: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
  Stream #0:4(eng): Subtitle: ass
    Metadata:
      title           : *****
      BPS-eng         : 659
      DURATION-eng    : 00:21:56.020000000
      NUMBER_OF_FRAMES-eng: 599
      NUMBER_OF_BYTES-eng: 108427
      _STATISTICS_WRITING_APP-eng: mkvmerge v31.0.0 ('Dolores In A Shoestand') 64-bit
      _STATISTICS_WRITING_DATE_UTC-eng: 2019-03-06 18:09:34
      _STATISTICS_TAGS-eng: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
  Stream #0:5: Attachment: ttf
    Metadata:
      filename        : Lato-Bold.ttf
      mimetype        : application/x-truetype-font
  Stream #0:6: Attachment: ttf
    Metadata:
      filename        : Lato-BoldItalic.ttf
      mimetype        : application/x-truetype-font
  Stream #0:7: Attachment: ttf
    Metadata:
      filename        : Chuu2-next.ttf
      mimetype        : application/x-truetype-font
  Stream #0:8: Attachment: ttf
    Metadata:
      filename        : 00243.TTF
      mimetype        : application/x-truetype-font
  Stream #0:9: Attachment: ttf
    Metadata:
      filename        : 01_tama.TTF
      mimetype        : application/x-truetype-font
  Stream #0:10: Attachment: ttf
    Metadata:
      filename        : CFMarieEve.ttf
      mimetype        : application/x-truetype-font
  Stream #0:11: Attachment: ttf
    Metadata:
      filename        : Nyarlko-Pinkthing.ttf
      mimetype        : application/x-truetype-font
Unsupported codec with id 98304 for input stream 5
Unsupported codec with id 98304 for input stream 6
Unsupported codec with id 98304 for input stream 7
Unsupported codec with id 98304 for input stream 8
Unsupported codec with id 98304 for input stream 9
Unsupported codec with id 98304 for input stream 10
Unsupported codec with id 98304 for input stream 11

Transcoded videofile

N/A

Merged videofile

ffprobe details 
Input #0, matroska,webm, from '*****.mkv':
  Metadata:
    title           : *****
    creation_time   : 2018-11-21T22:18:26.000000Z
    ENCODER         : Lavf58.76.100
  Duration: 00:23:41.95, start: 0.000000, bitrate: 2616 kb/s
  Chapters:
    Chapter #0:0: start 0.911000, end 139.925000
      Metadata:
        title           : Chapter 4
    Chapter #0:1: start 139.925000, end 810.929000
      Metadata:
        title           : Chapter 5
    Chapter #0:2: start 810.929000, end 1421.955000
      Metadata:
        title           : Chapter 6
  Stream #0:0: Video: hevc (Main), yuv420p(tv, bt709/unknown/unknown), 3840x2160 [SAR 1:1 DAR 16:9], 23.98 fps, 23.98 tbr, 1k tbn (default)
    Metadata:
      BPS-eng         : 1522424
      DURATION-eng    : 00:23:41.087000000
      NUMBER_OF_FRAMES-eng: 34070
      NUMBER_OF_BYTES-eng: 270437279
      _STATISTICS_WRITING_APP-eng: mkvmerge v31.0.0 ('Dolores In A Shoestand') 64-bit
      _STATISTICS_WRITING_DATE_UTC-eng: 2019-03-06 18:09:34
      _STATISTICS_TAGS-eng: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
      DURATION        : 00:23:41.086000000
  Stream #0:1(jpn): Audio: flac, 48000 Hz, stereo, s16 (default)
    Metadata:
      title           : Stereo
      BPS-eng         : 663155
      DURATION-eng    : 00:23:41.952000000
      NUMBER_OF_FRAMES-eng: 14812
      NUMBER_OF_BYTES-eng: 117871860
      _STATISTICS_WRITING_APP-eng: mkvmerge v31.0.0 ('Dolores In A Shoestand') 64-bit
      _STATISTICS_WRITING_DATE_UTC-eng: 2019-03-06 18:09:34
      _STATISTICS_TAGS-eng: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
      DURATION        : 00:23:41.952000000