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Just shooting in the dark, but:
What if you output your M4V file then determine its EXACT length.
Ouput your WAV file and use a Time Stretching effect (I'd use Sound Forge because that's what I'm familiar with) and make it match your video file.
4 seconds over 40 mins would not cause much pitch shift or other noticeable problems in the audio. Can't guarantee rock solid lip sync, but depending on the program material, it might be workable.
Could this be a DF versus NDF issue?
> Could this be a DF versus NDF issue?
Hmmm... every setting and Properties window shows 29.97... anything else I should look for?
> use a Time Stretching effect
I'll keep that in my back pocket for now. Doesn't seem like I should have to go to that length, however, but... Assuming the error in the source is relatively constant per AVCHD clip (maybe not a valid assumption, but seems reasonable), then the stretch effect would result in audio that was more or less out-of-sync depending on the density of cuts on the timeline.
Is it possible to create an audio-only TS using Premiere? Something that preserves the timing information? Seems not, but maybe there is. When I uncheck "Export Video", the option to create a TS seems to disappear :-(
>Could this be a DF versus NDF issue?
Unlikely. Drop Frame is a reference to the timecode (how frames are 'numbered'), not the running time (number of frames actually recorded).
Two five minute clips, one with DF and one with NDF, will have exactly the same running time and number of recorded frames.