I need to erase (silence) about 2 seconds of just one channel of a 2-channel stereo recording. I can use Audacity (or Ardour). I'm running Ubuntu 12.04.
In Audacity, you can approach this in at least two ways, depending on the nature of the bit you want to silence and the surrounding material.
The simple way is to highlight the section of the track / channel and select "Generate... Silence" from the menu. The suggested duration will be the length of your selection. This is a harsh edit, and very likely objectionable. You can ease that by insuring that your selection begins and ends at a zero crossing in the waveform. If you make the silence somewhat shorter and centered, you can fade out/fade in to soften the transition.
Another way would be to use 'envelope' mode, ramping down and up to cover the area. This is more or less the same thing as fade out/in above.
Again, depending on the nature of the sound, it might be possible to duplicate the channel you don't want to remove, into the silence you created. I'd do that by creating another track and copying the duplicate material, say from channel "A", into channel "B" and crossfading in and out of it.
I don't know if you ever got the answer you needed but I just found out how to do it. If you have a stereo recording in Audacity you click on "Audio Track" at the left of the stereo channel you're looking for. You'll see Split Stereo Track in the drop down menu and then you can edit a specific segment of the audio in that channel alone