I'm on the latest patch (according to Steam, as of 24 May 2018 AEST) -- this just happened to me.
I levelled up Eder to level 2, and suddenly the watcher became Eder too!
Is this reversible, or do I have to go back to my last auto-save?
And if I go back, what is the trick to NOT having Eder duplicate himself again? Is there some order of levelling up that is safer?