I have about 300 video files of an old TV program that I need to convert in AME. However, the files have audio only on the left channel, with an empty right channel. It is a mono mix, but on a stereo track. I know Premiere offers the "Fill Right with Left" filter, but is there any way to batch-apply this in Media Encoder to all 300 files, without needing to run them individually through Premiere?
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Unfortunately, no, there's no way to apply a Premiere Pro effect at the source level in AME. Although, this would make a great feature request.
Since the Fill Right with Left effect cannot be applied at the Master Clip level, you'd have to send each file from a Premiere Pro Sequence to AME. Doable, but not automated.
Changing audio channel configurations is something for the Batch Processing panel in Adobe Audition.
How to use Batch Processing & Scripting in Adobe Audition CC (Audio 101: Part 6)