Replace Audio during Batch Encoding?

Hi! I am converting hundreds of video files which get posted to YouTube. We remove the raw background noise using Encoder and apply a still watermark. This is good.

I would like to replace the audio with the same audio file, with a voice and our business music theme (no copyright issue). I do not see an option in Encoder to replace audio.

Does anyone have a workflow to do such a thing? I don't want to reformat the video file - just replace the audio. Has to be part of an "automated" process. Files go to a folder. Media Encoder does its thing, gets uploaded to YouTube with very little interaction by this tire human - because I am doing hundreds of these every few weeks.

Thanks!