This prompted me to go look at our site. I was able to log in today (using my AGOL admin account) to view our sites.
I upgraded one of our sites (which happened to be called "beta"), and it created a new copy of the site, changing beta to "beta2016-11-16t162849270z" and viewing the site shows the "Default" layout. Is that what you are seeing. I think this can than be modified, but it doesn't look like much copied over from the 1.0 site (I was not in beta for 2.0 that I am aware). Looks like it will take sometime to get it customized again.
I don't know if this is what you are experiencing or if you can't log in at all. If you can't log in, I would put in a tech support ticket since that may be something else.