Replace audio in WTV

[dejong12]

I have some recordings edited with VideoReDo to remove commercials, remuxing them back into wtv because of the FF/RW option and the metadata (show information). One problem is that I can't mute the first few frames of a show in VideoReDo. These frames often contain the audio of the last commercial before the start of the show I recorded, resulting most of the times in a beep or stuttering noise of a few milliseconds. I use AVS Audio Editor to delete that noise but now I want to mux that back into the cut wtv. I can't do this with VideoReDo, because if I use the Elementary Stream Muxer, I will lose all metadata and I will have audio problems at the start of the video. Is there another program or is it possible to replace audio with ffmpeg or something?