Possessed said:

In case you need to do ac3 editing beyond cutting the whole thing (such as muting a line but keeping the sound effects) the FREEWARE and excellent program Audacity now has full 5.1 ac3 support. No more hypercube transcoder and then wav to ac3 again, you can now just demux the ac3, edit in audacity, save and mux back again. I reccomend this, I've been using audacity for years for other audio, and now it has ac3.

Btw, it should be pointed out that Audicity's hype is misleading. You cannot work losslessly with AC3 (or mp3 for that matter).

If you are separating and then remerging channels from a lossy source, you are reencoding, it's just being done for you automatically.