Finally it worked.
Here is the code:
IDENTIFICATION DIVISION.
PROGRAM-ID.RemoveDup2.
ENVIRONMENT DIVISION.
INPUT-OUTPUT SECTION.
FILE-CONTROL.
SELECT INPUTFILEDUP ASSIGN TO 'C:\Cobol\INPUTFILEDUP.txt'
ORGANIZATION IS LINE SEQUENTIAL.
SELECT OUTFILEDUP ASSIGN TO 'C:\Cobol\OUTFILEDUP.txt'
ORGANIZATION IS LINE SEQUENTIAL.
SELECT WorkFile ASSIGN TO "WORK.TMP".
DATA DIVISION.
FILE SECTION.
FD INPUTFILEDUP.
01 INPUTFILEDUPREC.
88 EOFINPUTFILEDUP VALUE HIGH-VALUES.
02 INPUTFILEID PIC 9(07).
FD OUTFILEDUP.
01 OUTFILEDUPREC PIC 9(07).
SD WorkFile.
01 WORKREC.
02 WINPUTFILEID PIC 9(07).
WORKING-STORAGE SECTION.
77 WS-VARIABLE PIC 9(09) VALUE ZERO.
77 REC-NOT-MATCH PIC 9(01).
77 CUR-VARIABLE PIC 9(7) VALUE ZERO.
PROCEDURE DIVISION.
BEGIN.
SORT WorkFile ON ASCENDING KEY WINPUTFILEID
USING INPUTFILEDUP GIVING INPUTFILEDUP
OPEN INPUT INPUTFILEDUP
OPEN OUTPUT OUTFILEDUP
READ INPUTFILEDUP
AT END SET EOFINPUTFILEDUP TO TRUE
END-READ
PERFORM UNTIL (EOFINPUTFILEDUP)
IF INPUTFILEID NOT EQUAL TO WS-VARIABLE
MOVE INPUTFILEID TO WS-VARIABLE
WRITE OUTFILEDUPREC FROM INPUTFILEID
READ INPUTFILEDUP
AT END SET EOFINPUTFILEDUP TO TRUE
PERFORM UNTIL (EOFINPUTFILEDUP)
ELSE
DISPLAY "DUPLICATE FOUND " INPUTFILEID
READ INPUTFILEDUP
AT END SET EOFINPUTFILEDUP TO TRUE
END-READ
END-PERFORM
CLOSE INPUTFILEDUP
CLOSE OUTFILEDUP
STOP RUN.