Update to WordPress 4.6 deletes all widgets

Hi, I've discovered that all the widgets have disappeared after updating WordPress to 4.6.
I've made a few test and discovered the theme MO is creating the problem somehow. These are the test I've run so far:
1. Using a backup (WP 4.5.3) I've created 2 copies of the website at http://www.deboss.com.au/wp2 and http://www.deboss.com.au/wp3
2. I've disabled all the plugins in both websites
3. I've updated MO to the latest version (downloaded 3 Sep 2016), the only file that I've changed after that is wp-content/themes/Mo/css/orverride.css.
4. I've updated http://www.deboss.com.au/wp3 to WordPress 4.6 and all the widgets have dissapeared

Now I have 2 websites that are almost exactly the same, but http://www.deboss.com.au/wp2 hasn't been updated and all the widgets are still there, while http://www.deboss.com.au/wp3 has been updated and all the plugins disappeared.

Please help (I've created a user for you Piotr, sent it via PM)

Hi,

I've checked the issue twice - on my localhost and our project server and there's no problem after update to WordPress 4.6. Your widgets are removed completely or i.e. moved to "inactive widgets" section?

Hi Joshua M,
The widgets get removed completely

I don't think that the issue is connected with our theme directly. Unfortunately I can't reproduce it on my installation.

Could you try to activate another theme like default Twenty Sixteen, set some widgets, then try to update your WordPress to version 4.6?

Thanks for your quick response Joshua.
Ok, I'll try that once I get back, I have to go away for 3 weeks, but will get back to this case then.