Auto update and languages modifications

Hello, i have translated a part of plugin and when i auto update it i have to upload my translation again because of auto update.
How can i do to save my translation files from auto update eraser ?
I hae found this plugin http://wordpress.org/extend/plugins/translation-preserver/ but some themes/plugins use the same file name fr_FR.po and not plugin-theme-name-fr_FR.po