I use Premiere. I use tsmuxer to demux the video into its own .m2ts stream and the audio into its own stream, then import the separate video and audio streams into Premiere and link them together in the timeline. No reencoding involved as long as your timeline is set up properly (AVC/h.264 video of the correct resolution and framerate, or whatever video format your original file came in).
This also allows me to convert any incompatible audio independently from the video.