How to completely overwrite and replace the permalink rewrite rules?

The site I'm working on has a very specific permalink structure, one that is very different from the default wordpress permalinks. I don't want to add rules; I want to replace the rules entirely with my own custom array of rules.

Below is some quick and dirty testing code. (This is not production code, I know not to flush the rules on every page.) This code is located in my theme's functions.php.

/**
 * Flush the rules. Just for testing.
 */
function example_flush_rewrite_rules() {
    global $wp_rewrite;
    flush_rewrite_rules(); // Calls the function below
    print_r($wp_rewrite->rules); // Does not display my rules, shows default rules
}
add_action('init', 'example_flush_rewrite_rules');

/**
 * Overwrite the rewrite rules.
 * This does not work. :(
 */
function example_generate_rewrite_rules($wp_rewrite)
{
    global $my_custom_rules_array;
    $wp_rewrite->rules = $my_custom_rules_array;
}
add_action('generate_rewrite_rules','example_generate_rewrite_rules');

Both function are called correctly, but the rules don't change after loading the page. How do I overwrite the contents of wp_rewrite and the rewrite rules? What am I doing wrong here? Thank you!