Arrays.sort() removes many items from my array

Confirmed the 'artifact' behavior via the Online Java Compiler :

import java.util.Arrays;

public class MyClass {
    public static void main(String args[]) {
        // instead of using readFile() the array is defined here.
        // note the \n on the last element
        String[] states = {"FL", "GA", "SC", "NC", "VA", "MD", "NY", "NJ", "DE", "PA", "CT", "RI", "MA", "VT", "NH", "ME", "AL", "TN", "KY", "WV", "OH", "MI", "MS", "AR", "MO", "KS", "NE", "IN", "IL", "WI", "MN", "LA", "TX", "OK", "IA", "SD", "ND", "NM", "CO", "WY", "ID", "AZ", "UT", "NV", "MT", "CA", "OR",
           "WA", "AL", "HI\n"};

        System.out.println(String.join(" ", states));
        System.out.println(states.length);

        Arrays.sort(states);

        System.out.println(String.join(" ", states));
        System.out.println(states.length);
    }
}

And the Output:

FL GA SC NC VA MD NY NJ DE PA CT RI MA VT NH ME AL TN KY WV OH MI MS AR MO KS NE IN IL WI MN LA TX OK IA SD ND NM CO WY ID AZ UT NV MT CA OR WA AL HI

50
AL AL AR AZ CA CO CT DE FL GA HI
 IA ID IL IN KS KY LA MA MD ME MI MN MO MS MT NC ND NE NH NJ NM NV NY OH OK OR PA RI SC SD TN TX UT VA VT WA WI WV WY
50

Apparently the log used by @Arjun Kay had truncated the elements printed after the sorted element with the break-line character.

Your readFile method is sloppy. You declare a buffer array char[] cbuf = new char[200]; with 200 elements.

It sounds like your file is formatted with a state on each line:

FL
GA
SC
NC

You read the entire file into your buffer, but you don't fill the buffer so the trailing 50 elements are still initialised to the default null character value \u0000 (see this question)

cbuf = [F][L][\n][G][A][\n][S][C][\n][N][C][\n] ... [\u0000][\u0000]

Then you convert cbuff to a string:

all = "FL\nGA\nSC\nNC\n ... \u0000\u0000\u0000"

Then you split the string to convert it to an array:

array = [FL][GA][SC][NC]...[\u0000\u0000\u0000\u0000\u0000]

So you can see you have a bunch of useless characters in your final array, because your buffer was bigger than the file that you read.

I can't replicate your missing states on my machine, but you could clean up your file reader and I think it will work for you. Use a BufferedReader, then you can read your file a line at a time and it will save you all the manual splitting. I would also recommend using a List<String> instead of a String[] array, so you don't have to handle the size of the array.

Consider this:

public static void main(String[] args) throws IOException {
    String[] states = readFile("States.txt");

    System.out.println(String.join(" ", states));
    System.out.println(states.length);

    Arrays.sort(states);

    System.out.println(String.join(" ", states));
    System.out.println(states.length);

    // now do the same thing but using a list
    List<String> statesList = readFileToList("States.txt");

    System.out.println(String.join(" ", statesList));
    System.out.println(statesList.size());

    Collections.sort(statesList);

    System.out.println(String.join(" ", statesList));
    System.out.println(statesList.size());
}

// read the file to an array
public static String[] readFile(String FileName) throws IOException {
    String[] states = new String[50];
    BufferedReader br = new BufferedReader(new FileReader(FileName));

    String state;
    int index = 0; // keep track of the array index
    // when readLine() returns null there are no more lines to read
    while((state = br.readLine()) != null && index < 50) {
        states[index] = state;
        index++;
    }

    return states;
}

// read the file to a list
public static List<String> readFileToList(String FileName) throws IOException {
    List<String> states = new ArrayList<>(); // no array size to worry about
    BufferedReader br = new BufferedReader(new FileReader(FileName));

    String state;
    while((state = br.readLine()) != null) {
        states.add(state); // no indexes to worry about
    }

    return states;
}

you can use BufferedReader for reading a line from the FileReader like this

 public static String[] readFile(String FileName) {
        ArrayList<String> stringArrayList = new ArrayList<>();
        BufferedReader bufferedReader;

        try {
            bufferedReader = new BufferedReader(new FileReader(FileName));
            String line;
            while ((line = bufferedReader.readLine()) != null) {
                stringArrayList.add(line);
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
        return stringArrayList.toArray(new String[0]);
    }