I am not certain what result you want, so here are two options:
zi = find(X == 0);
X(zi) = [1:26 -2]'; % Option #1
X(zi) = reshape([1:26 -2], [], 3)'; % Option #2
EDIT —
Option #1:
X =
-1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-1 1 4 7 10 13 16 19 22 25
-1 2 5 8 11 14 17 20 23 26
-1 3 6 9 12 15 18 21 24 -2
Option #2:
X =
-1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-1 1 2 3 4 5 6 7 8 9
-1 10 11 12 13 14 15 16 17 18
-1 19 20 21 22 23 24 25 26 -2