Say you have a file in one of your modules for which you need a file object, the trick is to _copy_ it to the public filesystem, and then use it. For example, say we need to import the french translation of MYMODULE during an update, we can use the following code:
<?php
$file = file_save_data(file_get_contents(realpath(drupal_get_path('module', 'MYMODULE') . '/translations/fr.po')), 'public://temporary-po-import.po');
_locale_import_po($file, 'fr', LOCALE_IMPORT_OVERWRITE, 'default');
?>