A data storage device is disclosed comprising a head actuated over a disk. A first plurality of codewords and corresponding parity sector are generated, and a second plurality of codewords and corresponding parity sector are generated. The first and second plurality of codewords are written to the disk, and during a read of the first and second set of codewords, M codeword locations within the data track that are unrecoverable are saved, and N codeword locations out of the M codeword locations are selected based on a quality metric of the read. The N codewords are reread from the data track at the N codeword locations and reliability metrics associated with the N codewords are saved. The saved reliability metrics are updated using at least one of the first parity sector or the second parity sector.