How do you get Cartoon Animator 4 to render out part of a frame range and overwrite those frames in the fileset. It seems to just want to number them from zero.

Use these red pointers to mark the start and end of frame.
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YouTube Tutorials Here

Yes, when you set a frame range it automatically does that, but it does not overwrite the fileset with that exact frame number. It just renumbers say a set frame range of 100-200 to 0-100.