I have been struggling with style-highlights and character highlighting for a while now.
I would advise to avoid the default option:
Formatting: Save all formatting
See this thread: Character style lost on Compile, one cause isolated
It’s basically the worst of both worlds.
Now that I am trying to compile with that highlight intact, I will change my recommendation there from the paragraph-only style and into the character only style (you can’t change a Par-only into a char-only, need to make a new one).
If you use the Styles feature at the front, before you type/highlight, it will still set stuff right initially and let you overwrite the styling w/ italics, ect as you go. Trying to apply a character style after the fact will nuke your formatting. Para-only would be appropriate there, as some character styling will be spared.
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Right now, I’m in the process of removing the style-highlighting, instead swapping it to actual character highlight. If Scrivener allowed me to export Compile that kind of highlight, I would not need to do this.
Also, you are not crazy. I myself experienced the exact same culture-shock when trying to find solutions to my issues.
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Right now, I am struggling to get the Compile to behave and actually match the colors right.
PDF actually Compiles with the correct faint highlight, but .docx and .doc always change it into a max saturation / top row highlight color, which is atrocious.
If anyone reading this has experience solving this issue, please chime in. I’m going to keep poking around a bit for other existing threads that are close, but will probably need to make a separate topic asking for help if/when I can’t find existing talk of this issue.