I use Xmedia Recode to do exactly what you are wanting to do. First I export the audio from my avchd m2ts files as 24bit PCM wav files using Xmedia. I perform noise reduction on these in Audacity and export it as the same type of wav file. Then using Xmedia, I remux the video only from the m2ts file and the cleaned wav file into a new mov file. Works like a charm.