The problem is many have been living for generations without any documentation. How are they supposed to prove?
I do not know if that is a reasonable fear in this case because I do not know the general social attitudes in India right now, but how would you relax someone who is scared the same may happen again?
Fakhruddin Ali Ahmed's nephew was left out of the NRC for the second time. We can't even get our electoral rolls correct repeatedly; people who have voted from the same area for 40+ years are left out mysteriously.