I'm afraid we can't have our cake and eat it, as Necron players. If we consider base contact at the start of the fight phase to count, before challenges are issued, then that means you cannot subsequently use other wargear which occurs at the start of the Fight phase when a challenge is issued, because you've defined the start of the Fight phase before challenges are issued.
I'm pretty sure most people would rather suffer a Whip Coil than Mindshackle Scarabs.
In addition, the movement from the challenge is before the Fight phase and all it's done is moved models about so they can subsequently fight. As such the challenger and challengee only count as being in contact with each other still at the start of the Fight phase.
If you want precedent, check all the rulings in various FAQs where other models are forbidden from affecting an enemy challenger, even Wolves for SW characters.
So no, the Librarian shouldn't have been affected by the Whip Coils.