Give Matlab a go, there's quite a few resources out there to get you started but if you have programmed at all before you should be able to pick it up fairly easily, I've seen it used mainly in acoustics applications but I'm sure you could find another possibly more creative use.
Use sox. If you are using Windows, then you can install MobaXterm on your computer. Then install the sox using: apt-get install sox.
Invoking sox is very simple, just provide the start time and the duration to cut. For 2 minute chunk starting at 5m 32s you get:
sox in.wav out.wav trim 5:32 2:00
"Cakewalk Application Language (CAL) is an event-processing language based on C and LISP that you can use to extend Cakewalk products with custom editing commands. You can write your own CAL scripts, or use and edit CAL scripts that other people have written. You also can create CAL scripts by recording a series of commands, keystrokes, and ...
You can use protools 'strip silence' feature. This will allow you to set working thresholds in order to 'cut' audio regions/clips based on the audio level of the content. Strip Silence allows you to either remove the audio, or remove the silence.
As leftaroundabout said, use ffmpeg (or avconv - the one is forked off the other).
It is command line based, which makes it useful for batch operations.
On my Linux box the batch command would be something similar to:
for FILE in *.mp4
do ffmpeg -i $FILE $FILE.mp3
Use the -c:a copy option if you just want to strip away video and use the audio codec as-...
Reaper contains versatile batch processing capability:
Wavosaur does batch processing with vst chain processing (it's free):
Smack My Batch Up does the same thing with up to 5 chained plugins (also free). The author of Smack My Batch Up posted links to Mac versions here also.
as long as the files are lined up exactly into the same time position as the rendered file, you could easily use a quickkeys script to do this.
just group the tracks, tab, b, repeat.
IMO quickkeys is an invaluable addition to any daw for the macro looping capabilities.