The input file
FileInputStream file = new FileInputStream(new File("//Users//"+ usr +"//Desktop//TNA//input//FR-OPS-030 Master Training Plan_Rev4.xls"));
HSSFWorkbook workbook = new HSSFWorkbook(file);
is a different file to the output file
FileOutputStream outFile =new FileOutputStream(new File("//Users//"+ usr +"//Desktop//TNA//output//FR-OPS-030 Master Training Plan_Rev41w.xls"));
workbook.write(outFile);
So your are always appending to the original file, not to the updated file.
Why not just open it (and close it once)?