"Audacity will happily mangle the shit out of audio data. You can verify this by opening a .wav, writing it back out, and comparing the two files. It’s also fun to look at the spectrogram of an “empty” audio file that got passed through Audacity."

This is surprising. Has anyone else noticed this and identified a safer program to use?

It's a known issue, for example https://hydrogenaud.io/index.php/topic,96031.0.html from 2012 discusses it. You can render Audacity safe for lossless audio editing by changing the default "quality" settings to match your data format and disabling dithering.

Here's the settings I use for lossless editing of CD audio: https://i.imgur.com/a7VqOuj.png

That is interesting, it, would be good if there was a lossless mode that automated this.