Проверял, вроде все правильно выделяет
package com.javarush.task.task19.task1908;
/*
Выделяем числа
*/
import java.io.*;
import java.util.Arrays;
public class Solution {
public static void main(String[] args) throws IOException {
BufferedReader b = new BufferedReader(new InputStreamReader(System.in));
String f1 = b.readLine();
String f2 = b.readLine();
b.close();
BufferedReader b1 = new BufferedReader(new FileReader(f1));
StringBuilder str = new StringBuilder();
while(b1.ready()){
final StringBuilder append = str.append(b1.readLine());
}
b1.close();
String numberOnly;
numberOnly = str.toString().replaceAll("[^0-9]+", " ");
BufferedWriter b2 = new BufferedWriter(new FileWriter(f2));
b2.write(numberOnly);
b2.flush();
b2.close();
}
}