Writing a regex to split string

I would forgoe the part about the regular expression and work with the bare values here:

String[] numbers = string.substring(1, 9).replace(".", ":").split(":");
int value = Integer.parseInt(numbers[1]);
String result = "[" + numbers[0] + ":" + (value + 2) + "." + numbers[2] + "]";

That way you can later change other values as well.

If you always know that your two numbers in the center of the square brackets are going to be bounded by the same characters, and those characters will not appear elsewhere in the string, I would recommend using a simple substring instead of a regex.

For example:

public class AddToString {
  public static final char SEPARATOR_1 = ':';
  public static final char SEPARATOR_2 = '.';

  public static String getAddedString(String input, int add) {
    int pos1 = input.indexOf(SEPARATOR_1);
    int pos2 = input.indexOf(SEPARATOR_2);

    StringBuilder builder = new StringBuilder();
    builder.append(input.substring(0, pos1+1));
    builder.append(Integer.parseInt(input.substring(pos1+1, pos2)) + add);
    builder.append(input.substring(pos2, input.length()));
    return builder.toString();
  }

  public static void main(String[] args) {
    System.out.println(getAddedString("[00:25.30]", 2));
  }
}

This has no null checks or formatting checks, but it will get you started.

public String addValue(String string, int valueToAdd) {
    int newValue = Integer.parseInt(string.substring(string.indexOf(":") + 1, string.indexOf(".")));
    String stringToReturn = string.replaceAll(":*\\.", ":" + newValue + ".");
}

I would go for something like this:

String s = "[00:25.30]";

StringTokenizer st = new StringTokenizer(s,":");
StringBuilder output = new StringBuilder();
output.append(st.nextToken());
st = new StringTokenizer(st.nextToken(),".");
output.append(':').append(String.valueOf(Integer.valueOf(st.nextToken()) + 2));
output.append(".").append(st.nextToken());

System.out.println(output);