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Using ReplacePart and Cases as follows:

a = {{{0, 0}, {1, 7}, {2, 0}, {3, 2}, {4, 7}},
     {{0, 0}, {1, 0}, {2, 1}, {3, 2}, {4, 7}}};

patt = {x1_, x2_} /; x1 != 0 && x2 == 0;

ReplacePart[#, Thread[Position[#, patt] -> Cases[#, patt -> {x1, Na}, 2]]] &@a

(*{{{0, 0}, {1, 7}, {2, Na}, {3, 2}, {4, 7}}, 
 {{0, 0}, {1, Na}, {2, 1}, {3, 2}, {4, 7}}}*)