@maloki The part of the federated Atom feed that tells !GNUsocial which conversation (if the in-reply-to is unknown) it should be stitched into looks like this:
Which is an incomprehensible mess that I fully understand if @Gargron hasn't bothered trying to understand. (though I have a vague memory of him asking me about it, or someone else, and I couldn't give an answer. Maybe if I have enough sleep tonight I'll give a go at clearing the mess up tomorrow).