I was going to do another upgrade today to the latest nightly. But I also know my last one done about a week ago had also wiped out all my settings.
Can anyone confirm if this is a bug or new expected behavior?
And while I can add all bindings to the addons.cfg file, is there anything special needed or done to distinguish between 1.X and 2.0 bindings?
I remember I had lost all settings, transformations, actions, that were enabled, and had to re-enable habmin, habpanel, etc.
I just learned this myself. If there is no 2.0 version of the binding, just list its name (e.g. mqtt). If there is a 2.0 version of the binding but you want the 1.9 version append a 1 to the name (e.g. astro1). You must have the Legacy 1.x bindings option turned on.
I know the developers are working to ensure that having everything wiped out is being worked on but I donāt know the state of that. I also know that a few days ago a new update was made that moves a lot of configuration files from runtime to userdata (e.g. logging config) so even if this update does not wipe out your configs on its own, you may need to do so to get these changes (I did for my Docker instance).
For now, until they do figure out this upgrade process I would recommend using the text files (addons.cfg, etc) instead of PaperUI and Habmin.
Looks as if my experience I just made, fits into this topic.
So maybe this is useful information to someone:
I did sudo apt-get update && sudo apt-get upgrade and afterwards all settings Iāve done are lost.
openHAB-Dashboard has lost HABmin. After I reinstalled it, for example the dashboard I created still exists.
No bindings installed anymore.
All things I have added before I updated keep appearing in configuration > things, but are set to uninitialized.
After re-installing a lost binding, associated things are set to online again.
Some bindings seem to reinstall very slow, like sonos-binding, which is installing since about 5min and still ongoing at the moment.
For me the main issue was that the bindings havenāt been installed although I had specified them in the addons.cfg
Furthermore after installation of the bindings the things did not appear (this was the case previously and the links to the items were still operational.)
after my upgrade today (openhabian OH2-offline) I needed to create all things again. 
By default a new ThingID is generated so you need to pay attention to put in the old ID to ensure that the items are still linked correctly.
I hope there will be an easier way to upgrade without loosing all the settings.