How to edit misc/print.css without changing core
You don't need to edit any core file, to achieve what you are trying to do. Since you are talking of a theme, you just need to replace the template file used from the Book module. This is what done from the Stable theme, which has its own book-export-html.html.twig.

The only reference to the misc/print.css file is in book-export-html.html.twig; there isn't any core library with a reference to that file, and this makes things easier for a theme.
book-export-html.html.twig contains the following code.

  &lt;head&gt;
    &lt;title&gt;{{ title }}&lt;/title&gt;
    {{ page.head }}
    &lt;base href="{{ base_url }}" /&gt;
    &lt;link type="text/css" rel="stylesheet" href="misc/print.css" /&gt;
  &lt;/head&gt;


In the template file for your theme, you just replace it with the following, if you don't want to use any print.css file.

  &lt;head&gt;
    &lt;title&gt;{{ title }}&lt;/title&gt;
    {{ page.head }}
    &lt;base href="{{ base_url }}" /&gt;
  &lt;/head&gt;


If you just need to use a different print.css file for your theme, then you can simply edit the file path, and provide your own CSS file.

  &lt;head&gt;
    &lt;title&gt;{{ title }}&lt;/title&gt;
    {{ page.head }}
    &lt;base href="{{ base_url }}" /&gt;
    &lt;link type="text/css" rel="stylesheet" href="the_path_relative_to_the_theme_folder/print.css" /&gt;
  &lt;/head&gt;