codice:
        String newStr="";        
        String filePath= "U://test.txt";
        FileInputStream fis = new FileInputStream(filePath);
        String content = IOUtils.toString(fis);
       
        FileOutputStream fos = new FileOutputStream(filePath);
        IOUtils.write(content, new FileOutputStream(filePath));
        
        for (...) {
              newStr=...//recupera la stringa 
             
              content = content.replaceAll(content, newStr);
              fos = new FileOutputStream(filePath);
              IOUtils.write(content, new FileOutputStream(filePath));
        }
        
        fis.close();
        fos.close();

meglio?
Grazie