Okay, follow up - first, I'm not entirely convinced the (well-meaning) respondent on the TB forum is correct, because he suggested that TB has no way of knowing whether a local email matches a remote email (which would make IMAP sync impossible, so can't really be true).
Second, I just migrated another mailbox via mbsync
and this one looks fine in Thunderbird - which suggests that it is a mbsync
issue, quite possibly related to the "lost track" error that @vsajip mentioned, and which I have seen myself on previous migrations.
So, I'm either going to try via imapsync
instead next time, or might try and do future migration via creating new Thunderbird accounts and dragging the emails across. Unless a supported migration tool appears first. 🙂