It behaved really weird, first it started showing all correct number of pages crawled on old property, then I lost all the links which were there for old property in webmaster.
initially it looked like it was indexing all new pages as the crawled number increased in 2-3 days. Now after a week, number of crawled pages have drastically reduced to 642 from 2000 out of 3300.
It leaves me worried. I am working on it an will keep you updated.
meanwhile noticed DNS error as I was transferring new domain from one registrar to another.