What will happen if i change the checkpoint data from bitcoin source code and try to synchronice with blockchain?
It will think that the  databases have been corrupted and so it will attempt to redownload the entire blockchain. When it does, it will find that all of the blocks are invalid (because you changed the genesis block) and then it will just do nothing as it is unable to sync what it believes to be a valid blockchain.


  Is this what orphan block is?


No. Orphan blocks are something else entirely and unrelated.