How could to modify the permalink structure in all sites of the multisite at once?
You would probably need to do this programmatically, for example add a PHP file to your /wp-content/mu-plugins/
folder with this:
<?php
add_action('init', 'modify_all_permalink_structures');
function modify_all_permalink_structures();
if (isset($_GET['modify_all_permalinks')) {
$structure = '/%category%/%postname%/';
$sites = get_sites();
foreach ( $sites as $site ) {
switch_to_blog( $site->blog_id );
global $wp_rewrite;
$wp_rewrite->set_permalink_structure($structure);
$wp_rewrite->flush_rules();
}
restore_current_blog();
}
}
Then access yoursite.com/?modify_all_permalinks
to trigger it.
Recommend you do a full site backup first in case this is somehow insufficient. Remove the file when it has done it's job.