Avoiding transcoding ...

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Just to clarify, remuxing is not the same as transcoding. Remuxing when a client reports it is not compatible with the container is the expected behavior and remuxing uses *very few* cycles (i.e., small amount of CPU or GPU). Transcode/remux files in cache are temporary and cleared out on whatever schedule is set in your Scheduled Tasks. I would not fret about this, very much the expected behavior.