Hello Marcus, my initial post was a month ago; right now I don’t recall the details. But like I wrote in my post the problem occurred with comment notification emails; possibly with Jetpack, or out-of-the-box WP. In some cases I also use the “WP Better Emails” plugin. Rather than fixing several 3rd party plugins you maybe could modify your mechanism and add some conditions as to where you reduce links to root level?
Thanks for looking into this,
https://www.Holger.us