That is a lot of difference. I’ll try to figure out what might have happened.
As for 4.4.9 – I’m pretty sure the issue you’re seeing is the problem with losing the menu assignments. After switching to 4.4.9, you can open the Menu menu and re-assign your menu to primary or secondary. That got lost in the theme name switch – a WP feature that has been the bane of website users for years now. It is a “feature” called theme_mod that keeps some settings in a separate database entry, including menu assignments.