[HELP] Loading a new file does not scan audio on the new file?

[Mapsking]

OK, I did a movie today, and after it was finished, two of my subtitle tracks I worked hard on making are gone, not even in the recycle bin.  I have the debug log attached, hopefully you can fix this issue, because it is really annoying to lose a couple of days worth of work when I run a file through Hybrid.  I have some of the subtitles stored locally, and even though Hybrid did embed them into the .mkv output, it deleted 2 of them, and kept 1 in the original folder location.  It is quite irritating, not knowing whether or not the subtitles (.srt files) will still be there after Hybrid is done.

Thanks