Widget menus disapear randomly

Hello everyone,
I occasionally run into an issue where my sub sites which rely on widgets pulling custom menus into a template will be cleared randomly.

Example Screenshot: http://www.linuxbookpro.com/wp-content/uploads/2014/10/widgets.jpg

Error Example Screenshot: http://www.linuxbookpro.com/wp-content/uploads/2014/10/widgets2.jpg

Barring human error in the dashboard what can cause widgets to clear their saved information? Would updating a theme or plugin that enqueues the menu change the database in any way?

I’m just looking for possible reasons this could break not an actual solution.