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If you have a file that won't seek properly, you can "remux" it to generate a fresh index without losing any quality:

Download MediaInfo (GUI or CLI). Open your MKV and look under the "Menu" section. If you see "Seek head" list and "Cues" with a count >0, you have an index. If the "Menu" section is completely absent, you have no index. mkv index

: Occurs when the index identifies a track as the wrong language (e.g., "und" for undefined), which can be fixed by remuxing with MKVToolNix. Ripping Blu-ray and compress with ffmpeg If you have a file that won't seek