A method of operation of a storage system includes: identifying a low activity region in the first tier storage and a high activity region in the second tier storage; exchanging data of the high activity region with the data of the low activity region; and wherein protecting the data comprises: copying the low activity region to a reserved section; updating a new physical address of the low activity region in a virtual-to-physical table; copying the high activity region to the location in the first tier storage previously occupied by the low activity region; and updating the new physical address of the high activity region in the virtual-to-physical table and mapping the physical block region, originally allocated to the high activity region, to the reserved section.