Resale of flat and tax implications

Even if you had registered the flat on April 2011 (which i doubt would have happened), three years has not elapsed from that date to qualify into long term capital gains. The capital gains (if any) is short term in nature and will be added to your income and charged at normal slab rates. 

If you have claimed 80C (1 lac limit) deduction for your principal payments then property transferred within 5 years from the date of possession will disqualify those deductions. Those deductions will be liable to tax in the years you claimed those deductions.  

Deduction for reinvestment in another house property is available only in the case of long term capital gains, not short term capital gains. 

April 2012 Registration of flat is done.

This will attract short term capital gain, since you are selling it before completion of 3 years. 

My answer holds good since the reg is done on Apri 2012. 

Thanks.