Best way to flush_rewrite_rules for custom post type, in a mu-plugins plugin?

The flush_rewrite_rules function is reliable in some contexts like a theme or a plugin based on hooks but I’m not sure if it works for a mu-plugin

My statement is based on the fact that WordPress is initialized in this way:

• call the wp-settings.php file
• call the do_action( 'muplugins_loaded' ); hook, here your plugin is initialized
• call $GLOBALS['wp_rewrite'] = new WP_Rewrite(); here the method flush_rules is initialized and available from now on
• do_action( 'setup_theme' ); is called and I bet all my money that on this hook the flush_rewrite_rules will work

Solution?

Personally, I find reliable the deletion of the rewrite_rules option.

delete_option('rewrite_rules');

or

update_option('rewrite_rules', '' );

Whenever WordPress will lack the rewrite_rules it will build them back, this is also what the flush_rules method does.

There are points in WordPress execution flow where functions like this aren’t available. even in the core of WordPress I found this statement

// Rewrite rules can't be flushed during switch to blog.
delete_option( 'rewrite_rules' );

The only problem would be the performance, don’t do this on every request because it is a hard process to build them back.
As I can see you want to flush them only at the first call and this is a good thing.

P.S: I’m not such a self-promo fan but I’ve also written an article about this long time ago and I think it still stands up for this