Now Central Board of Direct Taxes (CBDT) has issued a circular, Circular No. 21/2016 on 27th May, 2016 by which it has been clarified that merely on the basis of excess receipt from commercial activity beyond the cut-off (20% of total receipts during the years, as of now), exemption u/s 12AA would not be cancelled.
Even though this was the understanding, it was never clearly articulated and no such direction was issued later. Therefore, this is a welcome clarification from CBDT.
To read the circular, please find the link here: http://fmsfindia.org.in/pdf/circular27052016.pdf