I didn't debug it yet what is the cause, but write the report to have a note of it: select a thread, mark it as watched. After a new sync, the messages become unread, even if they were markes as read. Seems to be backend independent (same with imap and maildir resource).
This bug has only been reported for versions before 4.14, which have been unsupported for at least two years now. Can anyone tell if this bug still present? If noone confirms this bug for a Framework-based version of kmail2 (version 5.0 or later, as part of KDE Applications 15.12 or later), it gets closed in about three months.
This is still present in 5.1.3.
I can confirm this still happens in KMail 5.13.3
I can confirm this also happens still on KMail 5.18.1