Last week we were asked to disable the "threads" in the comments and display them as a plain list in one of our projects, so checking in the Comment field settings we found an option which says:

"Threading: Show comment replies in a threaded list."

Which basically display the comments as a threaded instead of a list of comments. This option is marked on by default, so it seemed that it was just a matter of unchecking this option, but there was a problem with this, that setting did display the comments as a plain list, but in the code they were still being saved as a thread.

The main problem with this is if a comment is deleted and it has replies (even if the option of the thread is unchecked) all the replies are going to be deleted as well.

This is not a new problem there is an 11 year old issue and it seems that this has been happening since Drupal 4. The way to fix this so far was by using a contrib module called: Flat Comments The problem is that this module hasn't been ported to D8 yet.

We decided to fix that and port the module to help others with this problem. You can check the code here: https://github.com/agaric/flat_comments and we are in contact with the module's maintainer to create the D8 branch in drupal.org soon.

Expecting that this can help someone else.