Permalinks randomly break and start getting 404

I’m working on a WordPress instance with some plugins.

Everything works great after it starts serving 404 code. Seems to be random because everything works fine and in some moment the rewrite rules seems to break and the links stops working.

Sometimes it is happening when I update a content (we are using custom content types with this plugin https://wordpress.org/plugins/custom-content-type-manager/) but sometimes without touch anything (for example a weekend in the middle of the night).

We have been checking all the solutions we found but nothing works. The htaccess has the correct permissions and it is rewriting well the urls.

After debuging WordPress, the problem seems to be that for some reason, it is reseting the rewrite rules to other than the correct ones (here you can find both dumps, the one when the site serves 404 first, and the second one with the correct rules https://es.forums.wordpress.org/topic/permalinks-error-404?replies=5#post-53705).

Also, we check what was the wp-cron running but we didn’t find any plugin that touch the rules (I am not sure if WP doed anything with the rules periodically).

Thanks in advance.

Germán