They are co existing because they are a minority. It's the secular nature of Hinduism that makes it possible.
What happened in Muslim majority Kashmir - could Sunni Kashmiri's co exist there with Kashmiri pundits?.
The two nation theory doesn't say - Hindu's cannot co exist with Muslims - it clearly says Muslims cannot co exist with others. Which is a fact.
Kashmir is an aberration . so I would not take that example . what happened In Kashmir was complicated by the special status of Kashmir rather than the issue that it happens to be Muslim majority state ...
I believe Indian Muslims even if they attain majority will be able to live peacefully with people of other religions .
but that's my personal opinion ....