Navin Kabra <navin@smriti.com> writes:

>
> Specifically, I have a few threads/messages that don't have any tags,
> but still show up in notmuch search for those tags. And using notmuch
> tag to remove (or add) any tags on these threads has no effect. Doing
> a `notmuch compact` does not fix this issue.

0) As a first step, run xapian-check, something like

% xapian-check ~/Maildir/.notmuch/xapian

If your database is corrupted, there's not much notmuch can do about it
(except maybe make things worse).  I would think that compact would have
detected any corruption, but you never know.

>
>     ~$ notmuch search thread:0000000000058ca0 and tag:inbox
>     thread:0000000000058ca0  February 22 [1/1] Mandar Joshi; 
>     Announcing TiECon Pune 2017 - Pune's largest, most energizing 
>     startup event! ()

1) Can you also see the problem by looking at individual message-ids?,
   e.g. using notmuch show

2) In particular Does notmuch dump generate the correct output? If so,
   then dump your tags, rebuild your database, and reload the tags is
   one option.