MKV files have lost audio, please help!

[MalusCalibur]

I've been using LLC to trim .MP4 stream recordings for quite some time with no trouble, but recently I've been working with a batch of .MKV videos. As I have so many of these files to work with I tend to process them quite quickly and, unfortunately, don't religiously check every output afterwards before deleting the original. Imagine my horror when I tested one of these and realised to that the exports had no audio when played in VLC...
I've tried recovering the original files, but several 'data recovery' programs have all failed to find them despite some of the ones in question being deleted only yesterday (not to mention many of said programs don't let you actually recover anything anyway without paying). Searching online I found a number of suggestions to convert the MKV's into MP4's or otherwise 'repair' them (through VLC itself, through other programs, through online services etc), but none restore the sound. Sadly it is also not as simple as switching the audio track in VLC, as there is only one option for that (simple.aac).
Since LLC does not re-encode anything I find it hard to understand how the audio has been lost in this way (perhaps a setting within LLC that I've not seen fit to alter?), and reason that the trimmed files must still have that data in them somewhere, but I'm at a loss as to how to approach it, much less fix it.

Please, can anyone shed any light on this, and possilbly provide a solution?