Switching Default Audio Channel, Maintaining Subtitles

[videokinect]

So I have a project that I am trying to resolve;

I have a few thousand video files with various languages on different audio streams and several different languages available as subtitles.
These video files are not uniform in the sense that sometimes there will be 3 languages on different channels.  Sometimes just 2.
Sometimes English will be Channel 1, sometimes English will be Channel 2.

These video files get organized in various ways for presentations into playlists and its not a workable solution to just switch the audio channel as needed using the video player itself.

What I need to do is change all the audio channels to have the preferred English Audio channel to 1.
But I also need to maintain the subtitles for the hearing impaired (or for a multilingual group)

Is there some avenue/software that this is best accomplished?
With Avidemux I can pretty easily switch the Audio channels (time consuming, since I can only do it one file at a time)
But with Avidemux I seem to lose the subtitles even if I do nothing to them.

I guess a way to simplify my question is;
Is there anyway to switch the audio channels without messing with the subtitles at all?
Is there anyway to switch the audio channels of 10, 100, 1000s of videos at once without messing with the subtitles?

If Avidemux does not have a solution for this, anyone successfully solved this type of issue using another approach?

[eumagga0x2a]

As you already noticed, Avidemux doesn't support subtitle streams. You could use command-line ffmpeg instead (see -map) for remuxing the videos while keeping subtitles and ffprobe or mediainfo to identify available audio streams.