А если так?

package com.javarush.task.task18.task1826;

/*
Шифровка
*/

import java.io.*;

public class Solution {
    public static void main(String[] args) throws IOException {

        if ("-e".equals(args[0])) {
            codding(new FileReader(args[1]), new FileWriter(args[2]));
        }
        else if ("-d".equals(args[0])) {
            enCodding(new FileReader(args[1]), new FileWriter(args[2]));
        }
    }

    private static void codding(Reader reader, Writer writer) throws IOException {
        while (reader.ready()) {
            int temp = reader.read();
            if (temp != 65535 && temp != 0) {
                temp++;
            }
            writer.write(temp);
        }
        reader.close();
        writer.close();
    }

    private static void enCodding(Reader reader, Writer writer) throws IOException {
        while (reader.ready()) {
            int temp = reader.read();
            if (temp != 65535 && temp != 0) {
                temp--;
            }
            writer.write(temp);
        }
        reader.close();
        writer.close();
    }
}