I'm not aware of any way to change the audio inside an H.264 file without recompressing. Not a Mac user so don't know if CS6 will export to ProRes, but if not, you can use install and use the Avid DNxHD codec. Going to a high-quality intermediate codec should be a visually-lossless process and the resulting files with hold up better to color grading, keying, compositing, etc. than would a camera-native codec that is very highly-compressed.
Safe Harbor Computers
The Merge Clips command was made to combine separate video and audio into one clip within PP. Is this not sufficient? Why the new file?
The reason I want a new file is to archive interviews particularly.
I have a good amount of them that I wish to archive.
I have recorded these on DSLR - h264 alongside reference audio from the camera with additional audio into a Zoom h4.
Rather than having to refer back to a project file, i'd rather pick up a new file of the 'improved' version if you like.
That's how I see being most efficient for archiving purposes.