Audio does not play .mkv files on iPad/iPhone any more - used to - Video fine

The MKV files probably have a dolby audio codec. Support for dolby audio codec was recently removed. See the KB article on the issue below. You may need to reencode the videos using a different audio codec to get them to work. 

http://kb.sandisk.com/app/answers/detail/a_id/18851/ 

The (iXpand and Connect) apps do not currently support certain audio / video formats, such as those encoded with AC-3 (Dolby Digital) codecs. In some instances, you may be able to select the file and use the “Open in” feature to use other apps on your device that support such formats to playback these audio / video files.

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