Notes
 

I edited 12 of the 16 notes so I could look at them in-game. So I log in and I find many of my windows gone and those that were up with a solid black background. The UI looked odd. So I logged out and ran the updated and then the UI was back to normal. However, the notes were gone. I tested this again and each time I edit and save the note text and run the updater it is replaced with the original text. Is this a bug?

Nope, its working as expected :)
You're supposed to click the "do not update newer files" option within advanced options ;)

Ah. ok. But if I do that, what about the updates to the UI? How would I receive those?

Unless you're editing the other UI files, it won't affect them at all.