I need to go back to the Languages question.

Looking at the upgrade instructions, it seems to say I should upload the languages folder. Surely that is going to get rid of the adjustments I made to the language I used?

In the above post Gizmo says:
"Language files, don't upload language files when you upgrade, it will ask you to apply changes as needed."

Back to the official instructions, it only make me more confused:

Quote
The next screen will list the changes to the language files. If you uploaded a new copy of the "languages" directory in an earlier step, click the "I have updated my language files by hand" button. Otherwise, click the "Update my language files" button.

So, what EXACTLY do I do?
Can someone hand hold me through how I upgrade but keep my old changed language files?

Thanks