In a Matroska (MKV) container, the (or index) function as a map of the file. This index allows media players to "seek"—or jump to a specific timestamp—instantly without reading every byte of data sequentially from the start.
This is where mkclean comes in. This official tool from the Matroska Foundation rebuilds the file so that the index (cue element) is placed at the very beginning. Using it is simple: mkv index free