Ok, allow me to spell out the two ways of upgrading while dealing with language files.
You have two options...
You can choose to NOT upload the language files. While running the upgrade script, at the language step it will tell you what files are NEW, what need to be DELETED, and what need to be UPDATED.
You can tell it to manage the files on its own, in which case you will need to upload the NEW files to the language folder, and ensure all items within it are CHMODDED "666".
From here, it will delete the files it needs to delete, and update the language files which need to be updated.
You can choose to upload ALL language files, which will overwrite any changes you have made.
When you get to the languages section in the upgrade script you can have it do any updates it notices automatically, however, you'll want to ensure that all of the files in the directory are CHMODDED "666".
