Previously, when I played ES, The Deep had a distinct blue ring around the land-able space stations and planets. Not the purple-ish/bluish colour of Syndicate worlds and stations, a more vivid blue. With this most recent update, even after the events that separate north from south, The Deep stays red and labeled as REPUBLIC, rather than Blue and THE DEEP. Can someone please explain what happened, and if it was a conscious decision by the developer?

I don't think these planets have ever been labelled as anything but "Republic".
Is it possible that you were using a plugin that changed this, and the plugin was overwritten by the update?

To my knowledge it's the Shields Up plugin that makes the Deep its own government.