Rewriting empty sheets using poi doesn't produce almost any effect on modified
sheet. It means there are no values inserted, no styles applied to cells. Only
thing I can actually see in Excel are merged regions, and it means worksheet is
being really modified.
Way to reproduce:
1) Create empty Excel document (don't change anything),
2) Save to input.xls,
3) Compile and run this code:

import org.apache.poi.hssf.usermodel.*;
import org.apache.poi.poifs.filesystem.*;
import org.apache.poi.hssf.util.*;
import java.io.*;

public class Test2
{
	public static void main(String[] args)
	{
		try {
			HSSFWorkbook workBook = new HSSFWorkbook(new POIFSFileSystem(new
FileInputStream("input.xls")), true);
			HSSFSheet sheet = workBook.getSheetAt(0);
			HSSFRow row = sheet.createRow((short) 0);
			if (row == null)
				row = sheet.createRow((short) 0);
			HSSFCell tmpCell = row.getCell((short) 0);
			if (tmpCell == null)
				tmpCell = row.createCell((short)0);

			tmpCell.setCellType(HSSFCell.CELL_TYPE_STRING);
			tmpCell.setCellValue("XYZ");

			sheet.addMergedRegion(new Region(1, (short) 0, 1, (short) 1));

			FileOutputStream fileOut = new FileOutputStream("output.xls", false);
			workBook.write(fileOut);
			fileOut.close();
		}
		catch (Exception ex){
			ex.printStackTrace();
		}
	}
}

3) Open output.xls

You see empty sheet (without 'XYZ' string in cell(0,0)) with one merged region.

Version of poi:  poi-1.9.0-dev-20021122
Version of os/excel: windows2000prof/excel2002 (polish version)
Version of jdk: sun jdk 1.3.1
Compile command: javac -classpath ".\jakarta-poi-1.9.0-dev-20021122.jar"
Execution command: java -classpath ".;.\jakarta-poi-1.9.0-dev-20021122.jar"

Additional information:
There is simple workaround for this problem. Modify sheet in Excel putting (for
example) one space into cell(0,0).