I use notmuch with a set of Maildirs, synchronised with a remote IMAP
instance using mbsync. One of the folders I sync with is a "missed spam"
directory, which is used by the remote server to correct its own anti-spam
system. The server deletes the missed spam messages after it has added
them to its corpus of spam, which means that messages are regularly
deleted from that folder.

My impression is that notmuch is pretty smart about spotting messages
that have disappeared, but when I do notmuch show etc these days it
often comes up with a list of missing files, a la:

    Error opening /home/danny/mail/missedspam//cur/18403840321.foobar: No such file or directory

Is there any way I can correct the database to remove these entries?
Notmuch new doesn't seem to spot that they've vanished.

d.