‘Vous en êtes où?’ means Something like (in this context) ‘How far are you in your investigations?’.
So it’s just a way to get information on how Advanced is Something (as and object, a book or anything) or how Advanced is someone into Something (as an action, a research etc.).

might be a bit messy, but keep in mind it’s just to get news on Something.
‘Vous êtes où’ is ‘Where are you?’ so it can’t be associated with ‘Vous en êtes où?’.

‘Vous êtes où’ is used to get geographic informations when ‘vous en êtes où’ is used to get advancement state of Something.

Also ‘en être’ is not really used alone and it gets its sense with the sentence as a whole.

Vous êtes où would imply location— “where are you?”. Vous en êtes où gives a sense of “How far along are you?”—in a project, reading a book…and in this case, in an investigation. The en isn’t exactly translated as an English word by itself, like y often isn’t.