I think you're having the same issue I had with the clues.Must have missed it, I have not found all the clues to Nell and the Fairy Queen, I have tried all the clues I have to get Nell to see who her Mother is, but I must have missed one or more. The guide I did find never got to a place to tell you to work on her origin secret, so I can't get the clue I need to help the Queen. Anyone could help with this?
The final clue I was missing for this particular secret was hidden with the Fairy Queen herself: talk to her about the Prophecies, and it will reveal something about her and Nell.
A bit counter-intuitive that one
If it's not that, I don't know I'm afraid
The other pieces of this puzzle are with Nell and Samarra, but you should have thos already if you already know what Nell's dark secret appears to be