It's all fine now. I had them send me a new Nexus card (where it says I'm a Canadian). Then I kept calling the Nexus Enrollment Centre to have them remove *any* references to my previous citizenship, which they said they can't do...but then finally, an agent said she can add a detailed note in their system saying that I am no longer an Indian citizen etc etc.
Ever since then, no issues at all. I have TSA Precheck too.