Hi Nicolas
I have looked into the modifyOrder function and the save and loadLocale function in order.php file, and everything appears to be as it should. This issue also seems to affect the paypal payment plugin as the confirmation emails sent from there after the payment has been processed aren't translated either, even though the initial "order placed" email was sent in the correct language.
In my attempt to locate the issue, I also noticed that when changing an order status manually in the backend and set the "notify customer" to yes, the email is translated but the subject is not. However, if you view a specific order in the backend and click on the "Email" button (Next to the invoice, shipping invoice and back buttons), neither the subject or email are translated.
It worked as it should before we updated from 3.0.1 to 3.1.1, so the update seems to have broken that functionality