Confirmed 6.2 Software Update via Amazon Support Site
Here is what I know:
1. It removes root functionality, including the SuperUser.apk
2. It removes the Google Market app (some people say theirs is still working after update, so it could be how it was added/installed) and some of the other Google sync apk's that reside in /system/app (probably because that whole directory gets overwritten).
3. It overwrites the framework-res.apk file, so any customizations that were made to it (battery charge icon, custom wallpaper etc.), will be wiped out.
4. If you removed built-in apps like Facebook and IMDB before the update, they will have re-appeared again.
With some testing from Veritass (someone brave enough to try re-rooting again after the update), it is now pretty much back to normal. The steps I took to get there were:
1. Re-root using the standard SuperOneClick method we are all used to
2. Re-added the following apks in /system/app and applied the correct permissions:
Everything else was still working BEFORE I re-rooted, as the GoogleServicesFramework.apk remains intact and running. This includes, but is not limited to Gmail, Maps, Calendar, YouTube, Translate, Finance.
So, all is well again, and it didn't really mess up too much (that I can see). A minor inconvenience for no particular gain as far as I can see.
1. Amazon Video still doesn't work when rooted
2. The stock Carousel app still won't allow you to remove apps (not that I care about that myself, but you'd figure that a fix was imminent as this was a major gripe for a lot of users!)
3. Auto brightness is still not enabled