I find the easiest way is to use Megui. It converts the audio file to pretty much wahtever you want. I tend to convert AAC to AC3 and then merge with MKVmerge selecting the original video file and the new AC3 file.
For Megui In the audio input field select the whole video file, and for the audio output select the file type and encoder. I usually select AC3 using the Aften encoder. This keeps the original file untouched and creates an AC3 file.
In MKVmerge, select the original video file and AC3 file. This will then give you the option of 1x video track and 2x audio tracks. Select the video track and new AC3 track and merge togethor! Done!!