我重写了上面的代码如下，它工作正常。

public static void mergeFile() throws IOException {
   long unixTime = System.currentTimeMillis() / 1000L;
   final String sysName = String.valueOf(unixTime);
   File directory = new File("src/raw/");
   File[] files = directory.listFiles();
   FileWriter myWriter = new FileWriter("src/ok/"+sysName+".txt");
   for(File file : files) {
      String aLine;
      String fileName = file.toString();
      int split  = fileName.indexOf(".");
      long fName = Long.parseLong(fileName.substring(15, split)) ;
      if (fName <= unixTime) {
         FileInputStream fis = new FileInputStream(file);
         BufferedReader in = new BufferedReader(new InputStreamReader(fis));
         while ((aLine = in.readLine()) != null) {
              myWriter.write(aLine);
              myWriter.write("\n");
            }
            in.close();
         }
         Files.move(Paths.get("src/raw/"+fName+".txt"),
                    Paths.get("src/old/"+fName+".txt"));
      }
      myWriter.close();
      Query.insertSyslog("src/ok/"+sysName+".txt");
}