I know clock, radio presets are probably lost. But what about: Saved addresses in the Nav Vehicle settings (lights, door lock preferences) Reverse beep disablement
From what I understand is that you will lose the radio presets and the window auto up/down function. I have not heard of anyone losing any of your other list. Someone that has disconnected their 12V battery will need to chime in. To reset the windows, raise the window to the top and hold for a couple of seconds then lower to the bottom the same way.
I have had mine disconnected a couple of times and the only thing I remember loosing is the audio system presets. The ICE ECU probably resets also and it may take a few miles to readjust itself. Everything else including Nav and Bluetooth seems to use NV RAM.
I don't think I lost any of them either, but it has been a couple of years since I had it disconnected.
I know when I upgraded my Nav DVD I was wondering about losing cofiguration settings, phone pairings, phonebooks, etc. I was pleasantly surprised that all of that info was stored in memory outside of the DVD. The only thing I remember having to reset was my Region of the country. So, like tumbleweed, I would not think you would lose the phonebook settings.