Notmuch removing messages from the index, when calling `new` two times in a row

[David Bremner]

Mayeu <m at 6x9.fr> writes:
> 3. launching `notmuch new` right after, without having done anything else
>    on my Maildir folder:
>
>    Cleaned up 5 of 156 directories (1m 9s remaining).                                                                                                   
>    No new mail. Removed 22211 messages. Detected 378 file renames.

This message means that notmuch thinks 156 directories have been
deleted. Do you have any special mounts / symlinks / file systems that
might trigger this?

d