Laur Aliste <laur.aliste@gmail.com> writes:

>
> query:
>     notmuch search folder:work/Trash '*'
>
[snip]
> [new]
> tags=new;cal;
> ignore=Trash;trash;junk;Junk;Spam;spam;

That looks suspicious. If you're ignore Trash that explains why no
messages were found after re-index.