For some years the language codes TYPO3 used for translations where based on the ISO country codes - not the ISO language codes! That was changed with TYPO3 4.6. That's why it might happen that translations go missing on the website if you do not move the language files correctly after updating from TYPO3 4.5.
This issue gets even more confusing if you use snowbabel. For some time they also used the faulty language codes from TYPO3 4.5, but then switched to the new labels in version 3.6.2. There you can also lose your translations if you don't take the proper actions.