There is a bug in the current version of Widget Context that prevents unused widget areas from disappearing. I submitted this support request
a week or so ago and have already received a reply from another user who managed to create a fix. He submitted the fix for addition to the main plugin and it has been accepted, we just don't know when the update to the plugin will be released.
Temporarily, you can either roll back the plugin to the previous version and wait to update, or you can grab the updated code from the link provided by Gene in his response.