Dual registration of same flat. Isnt the 2nd registration void

Builder sold flat to Mr. X. Registration done between Builder and Mr X at Bhiwandi registration office in April 2016. Payment made by Mr. X to the builder, partly by loan and partly by cheque. Mr X decided to cancel the flat due to personal reasons. In Jan 2017, Mr. Y booked same flat allotted to Mr. Y, registration also done but between builder and Mr. Y. When Mr. Y wanted to take possession of flat, he came to know about this. When Mr. Y confronted the builder, builder said that you need not worry as they have a letter from Mr X that he is canceling the flat booking and also in next 2 weeks, the registration agreement between builder and Mr X will get cancelled with registration office. Money received from Mr. Y will be used to repay the loan taken by Mr. X and property will be peacefully transferred to Mr. Y along with loan closure letter. Registration office doesn't even check before registering the flat in 2 names? Isn't 2nd registration void ab initio?