I just upgraded my 'Custom Sidebars' plugin (note: I'm not using "pro").
Funny, but the custom sidebars I created before have all been moved to "Inactive Sidebar" in the Widgets area. I can't see any way to re-activate them or whatever I need to do.
The sidebars still display on the various pages I originally assigned them to. But the option to create a new custom sidebar has completely disappeared. In fact, custom sidebars have completely disappeared from the "Appearance" area of my Admin.
I'm using Custom Sidebars 126.96.36.199 and Wordpress 3.9.2