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This is mostly a workflow issue, and it sounds like you've figured out that it's better to make those significant changes first before splitting the clip into other sections. Use this from now on and you'll save yourself time and headaches ๐
I guess my question is based on that I'm used to work with DAWs primarily. There you can split the soundbites, replace, glue them together and so on independently on each track.
I usually use the same chroma key background, but this time I got a new idea that was more suitable in this particular case. That's something you cannot decide beforehand. Ideas pop up when you least expect it. ๐
But I agree that good planning is to prefer, that's how I work most of the time. ๐