Do extra plugin files get deleted during an upgrade?

I learned from a previous question that plugin updates are downloaded as a zip file, and WordPress overwrites every file in the plugin folder whether or not that file actually had a change from one version to the next. My question is, if the user has added extra files to the plugin folder (such as .po/.mo files for language translation), will those files be deleted during a plugin update?

Yes, the entire old directory will be deleted. So store files in the upload directory and other data in the database to keep all changes.

From class Plugin_Upgrader:

//Hooked to upgrade_clear_destination
function delete_old_plugin($removed, $local_destination, $remote_destination, $plugin) {
    global $wp_filesystem;

    if ( is_wp_error($removed) )
        return $removed; //Pass errors through.

    $plugin = isset($plugin['plugin']) ? $plugin['plugin'] : '';
    if ( empty($plugin) )
        return new WP_Error('bad_request', $this->strings['bad_request']);

    $plugins_dir = $wp_filesystem->wp_plugins_dir();
    $this_plugin_dir = trailingslashit( dirname($plugins_dir . $plugin) );

    if ( ! $wp_filesystem->exists($this_plugin_dir) ) //If its already vanished.
        return $removed;

    // If plugin is in its own directory, recursively delete the directory.
    if ( strpos($plugin, "https://wordpress.stackexchange.com/") && $this_plugin_dir != $plugins_dir ) //base check on if plugin includes directory separator AND that its not the root plugin folder
        $deleted = $wp_filesystem->delete($this_plugin_dir, true);
    else
        $deleted = $wp_filesystem->delete($plugins_dir . $plugin);

    if ( ! $deleted )
        return new WP_Error('remove_old_failed', $this->strings['remove_old_failed']);

    return true;