Steps to replica weird problems with GIT checkout @locaweb.

example.sh

#!/bin/sh
cd ~
# clona o repositório problemático
git clone repo test_repo
cd test_repo
# git status mostrará arquivos deletados, mesmo o repositório tendo acabado de ser clonado/checkoutado.
# ls mostrará que de fato os arquivos não existem, também.
git status
# checkout, reset
git checkout .
git reset --hard
# arquivos permanecem "deletados"
git status
# checkout manual de um destes arquivos não funciona também. git status ainda exibirá que o arquivo está deletado.
git checkout wp-content/themes/rb2portal/functions.php
git status

# somente os arquivos mostrados como deletados no status inicial possuem este problema; checkout funciona normalmente com outros arquivos. por exemplo:
echo "" > wp-content/themes/rb2portal/single.php #remove conteúdo
cat wp-content/themes/rb2portal/single.php #okay, conteúdo foi removido
git checkout .
cat wp-content/themes/rb2portal/single.php #conteúdo foi restaurado, exatamente como deveria ser.

# os arquivos afetados são os seguintes:
# wp-content/themes/rb2portal/acf_time_picker/js/option.php
# wp-content/themes/rb2portal/external/acf_time_picker/css/admin.php
# wp-content/themes/rb2portal/external/acf_time_picker/system.php
# wp-content/themes/rb2portal/external/eventos-post-type.php
# wp-content/themes/rb2portal/functions.php
# wp-content/themes/rb2portal/tag.php
# wp-content/themes/twentyeleven/colors/user.php
# wp-content/themes/twentyeleven/content-gallery.php
# wp-content/themes/twentyeleven/content-image.php
# wp-content/themes/twentyeleven/content-link.php
# wp-content/themes/twentyeleven/images/functions.php
# wp-content/themes/twentyeleven/inc/option.php
# wp-content/themes/twentyfourteen/image.php
# wp-content/themes/twentyfourteen/languages/info.php
# wp-content/themes/twentyfourteen/languages/options.php
# wp-content/themes/twentyfourteen/sidebar-content.php
# wp-content/themes/twentyfourteen/taxonomy-post_format.php
# wp-content/themes/twentyten/archive.php
# wp-content/themes/twentyten/author.php
# wp-content/themes/twentyten/images/dump.php
# wp-content/themes/twentyten/images/headers/include.php
# wp-content/themes/twentyten/loop-single.php
# wp-content/themes/twentyten/sidebar.php
# wp-content/themes/twentythirteen/author-bio.php
# wp-content/themes/twentythirteen/content-none.php
# wp-content/themes/twentytwelve/comments.php
# wp-content/themes/twentytwelve/index.php
# wp-content/themes/twentytwelve/js/diff.php
# wp-content/themes/twentytwelve/js/menu.php
# wp-content/themes/twentytwelve/single.php