Here's how I handle high def. variable audio and/or video.
Open in avidemux, cut on "I" frames...a little off beginning and end.
Use copy audio and video...export as ts.
Then use tsmuxer, demux audio and video wanted then remux in tsmuxer
I check after trimming and remuxing to make sure there is little or no audio delay.
This has worked for me, there may be other ways to do this that are superior.
Might could try cutting ends in Avidemux, and then save (export) audio first and then save (export) video and then see if tsmuxer will remux correctly to blu-ray.
But I haven't tried this route.
If BDtoAVCHD can open the mkv without crashing, it has the built-in tools to author to disc though I haven't used it to see how it works with mkv, the mkv needs to be somewhat blu-ray compliant for the program to work with it.
Any of the above supposes the files are somewhat compliant to blu-ray/AVCHD standards.