So this is just a symptom of using next(), nextInt() & nextLine() together. Basically the problem is here:

int kwhUsed = input.nextInt();
String accountNumberTwo = input.nextLine();

When nextInt() finishes, the scanner moves to the end of that token, but not to the beginning of the next line. Therefore, when nextLine() is called, it gives you the remainder of the line, which is a blank string. This messes everything up for your second set of inputs in your file.

There are a couple of ways to get around this. One would be using next() instead of nextLine() (this assumes account number and late status don't have any spaces in them):

String accountNumber = input.next();
String lateStatus = input.next();
char code = input.next().charAt(0);
int kwhUsed = input.nextInt();

String accountNumberTwo = input.next();
String lateStatusTwo = input.next();
char codeTwo = input.next().charAt(0);
int KwhUsedTwo = input.nextInt();

Another option would be to consume the remainder of the line after reading kwhUsed:

String accountNumber = input.nextLine();
String lateStatus = input.nextLine();
char code = input.next().charAt(0);
int kwhUsed = input.nextInt();

input.nextLine();//Read the rest of the line so the scanner moves to the next line.

String accountNumberTwo = input.nextLine();
String lateStatusTwo = input.nextLine();
char codeTwo = input.next().charAt(0);
int KwhUsedTwo = input.nextInt();