I have kept a separate thread for the analysis.Just my take on how he reached the conclusion. Detailed analysis you can read in the thread. But I would say it was Dr Dayal who sealed the nail on the coffin of Durga's freedom.
Dev had some theory around Durga and Nithya. But so far his confrontations with Thakurs had not yielded any positive results as they just evaded it effectively.
So after getting that car number he played around Dr Thakur first telling he killed Nithya and when Dr Thakur firmly said Nithya is alive he just put forward his theory
I am damn sure Dev didn't had any proofs to back his theory. But the way Dr Thakur stood silent over his theory and hugged him he knew his theory was right. Dr Dayal should have shouted, asked him where he thinks Nithya is, what proof he has on where Dr Dayal had hidden Nithya. He didn't do that and in a way without breaking promise to Durga, without telling he told Dev Durga is Nithya.
And Durga was gone the moment he called her Nithya. And I guess if there was any resistance in her that also fell by the side the moment he told " Love you Durga" in affirmation of his acceptance of her new persona.