You are calling it too early. Try calling it after init or even better bp_actions hook.

Regards
Brajesh

Hi Tosin,
This is doable but these are all steps in wrong direction.

You should try to troubleshoot and try to find the root issue. That will save you from a lot of troubles in future.

Regards
Brajesh

Hi Tosin,

It is fine to use the flush rewrite rule son theme change or some action which done not happen too frequently.

Also, My suggestion for you will be to find out the real culprit. Putting patches like this will lead to a fragile and unstable/unpredictable code.

Regards
Brajesh

Hi Nik,
You are welcome.

oops, I mean, you add a flag(meta key) and use that to filter the list of groups.

Regards
Brajesh

It’s a bad idea.

1. You should never flush rewrite rules on each request. That will hit the performance badly.

The last one is slightly better but still not recommend. why do you want to automate the permalink structure on theme activation?

It will take only 30 second to update it manually.

If you still want to do it, here is a cleaned version of your last one

function set_custom_permalinks() {

	if ( get_option( 'permalink_structure' ) ) {
		return;
	}

	global $wp_rewrite;
	// Save permalinks to a custom setting, force create of rules file
	$wp_rewrite->set_permalink_structure( '/%postname%/' );
	$wp_rewrite->flush_rules( true );
}

add_action( 'after_switch_theme', 'set_custom_permalinks' );

Regards
Brajesh