It's all an old story now, but if I should come to such an issue, I would probably try to use ffmpeg to transcode the audio (maybe to PCM) and keep the video intact, to save time.
Otherwise, if the sound seemed O.K. on DCP-o-matic, I would export to mp4, or ProRes first, and then try to make a DCP out of that.
Otherwise, if the sound seemed O.K. on DCP-o-matic, I would export to mp4, or ProRes first, and then try to make a DCP out of that.
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