It handles it gracefully. The tool cannot edit them, but it will ensure it does not mess them up.
Some examples:
- Table of contents can't be updated via the API. But the tool will ensure that the ToC doesn't disappear
- Styling can't be represented in markdown. That's fine - new content in the same paragraph will inherit the styles. The tool won't change the styles.
The core approach - don't mess with anything that isn't represented in markdown.
The way it works: we take the original google document and only apply the specific changes that the author intended to make. So this ensures we don't change anything else.