String dna[] = {"ATCTA"};
 int i = 0;
 dna[i] = dna[i].replace('T', 'C');
 System.out.println(dna[i]);

This works as expected. Double check your code if you follow a similiar pattern.

You may have expected, that dna[i].replace('T', 'C'); changes the content of the cell dna[i] directly. This is not the case, the String will not be changed, replace will return a new String where the char has been replaced. It's necessary to assign the result of the replace operation to a variable.

To answer your last comment:

Strings are immutable - you can't change a single char inside a String object. All operations on Strings (substring, replace, '+', ...) always create new Strings.

A way to make more than one replace is like this:

dna[i] = dna[i].replace('T', 'C').replace('A', 'S');

for (pos=0;pos<array.length;pos++) {
    if(array[pos]==null) {
       array[pos]=xyz
    }
}

The change you make is being overwritten by the draw method.

        clearBoard[row1][col1]='.'; // this will print out the 4 row variable values            

It's not clear to me what you're trying to accomplish in this method, since the comment completely disagrees with the code - you're setting the values to a period, not printing anything out at that line.

There's a lot of style things to improve here as well - a method named draw should not have the side effect of resetting the board.

I suspect your question is "why is chaining .replace acting oddly" and the array is not changing. You can prove that replace does not change the array quite easily:

    System.out.println(Arrays.toString(list));
    encrypt("abc");
    System.out.println(Arrays.toString(list));

So what is going on with your code? Each time you replace a letter you end up with a new string, that again you replace letters on. I don't have your full source code so I'll show with a real simple version:

a = a.replace("a", "b");
a = a.replace("b", "c");
a = a.replace("c", "d");

For "abc" is.... 'ddd'.

The answer to this is to look at each letter at a time and change it. Loop through the string and create a new one.

You have to write

fillWord[i] = charInput;

And two lines later

System.out.println(fillWord);

You printed your repeatChecker, not the fillWord.

Try using break.

for(int i = 0; i < array.length; i++) {
    if(fruit[i] == 0) {
        fruit[i] = X;
        break;
    }
}

This will ensure only one is changed, max.