If someone clicks "Reply" and changes the Subject, then Thunderbird (and pretty well every other e-mail program), will still think it belongs in the same thread as the original e-mail. That's because when you click "Reply", a header in the new e-mail references the original e-mail.

The solution is to start a new e-mail when you change the subject of the conversation.

Thank you for answer Bruce, but I'm 90+ % sure I have started new mails and not replied to existing ones. In one case it was new mail to completely different person about different subject. In other case and I have received new mail, which was then linked to existing thread. Now all 7 mails that belong to 3 different threads sit altogether in one thread... If sender will press 'reply' and then remove history and completely change the subject, will my client still know it belongs to existing thread?

Is there an option to remove reference from the header of particular email? so the chain is broken and client will start new thread. Thank you

I personally don't like seeing e-mails in threads, so I don't use it and don't have much experience with it. The only way I know of to break that chain, is to manually edit the headers of an e-mail to remove the "References:" header. That cannot be done in Thunderbird.

Maybe someone else here knows about this.

You can turn off seeing e-mails in threads for a particular e-mail folder: Thunderbird menu: View: Sort By: Select "Unthreaded". See my first snip below.