AE is not a good application for audio. Not at all. Freebee audio applications are often better.
I'd fix the audio in a different application. Since workflow for AE normally goes video editor - AE - video editor, I'd do it in the video editor.
I often render out fieles with NO audio, even when using lip-sync audio. I know it's already in the video editor.
Dave is right. If you're going to manipulate audio, do it in Audition or Premiere Pro.