Thanks for the quick response David.

xapian-check reports no problems.

Looking at individual message-ids using notmuch show does not show 
anything different. (In this case, the thread had just one 
message).

notmuch-dump seems to be working as expected, so I will try 
rebuilding my database from the dump in a few days, and report on 
whether that fixed the problem.

In the meantime, would anyone be interested in investigating this 
inconsistency so see if this is a notmuch bug that needs fixing? 
I'd be happy to run any commands and post the output.

thanks,
navin.