Performing fisher - yates shuffle directly in a 2D array

I have been trying, with no success, to perform a partial fisher-yates shuffle directly for the first N elements of a 2D array. I know I could transform the 2D array into a 1D array, perform the shuffle and then turn it back, but if possible I would like to avoid this.

The problem in my implementation is, I think although I have not proved it, that the last elements of each row of my array are not correctly shuffled. In fact, supposingI have a m*n array,of which the first N are equal to 1 and the rest m*n - N are equal to 0. When I perform my shuffle of the first N elements of the array, about 67% of the time the elements at the end of each row: array[i][end] are equal to 1, which seems to me to be too many times.

Here is my implementation:

void fisher_yates_shuffle(int n, int nbLines, int nbColumns, int **a) 
{
    for (int i = 0; i < nbLines; i++)
    {
        for (int j = 0; j < nbColumns; j++)
        {
            swap(a, i, j, i+rand()%(nbLines-i), j+rand()%(nbColumns -j)); // swap element with random later element

            n--;

            if(n<=0)
                break;
        }
    }
}

I know it doesn't look very good and there must be a more efficient way of doing it. Maybe there is a different, equally efficient algorithm to shuffle the first N elements of a 2D array like that?