I'm using apache's FTP client to upload file towards the ftp server. However the problem is there's the same tossed in the code however the file submitted is empty. What could trigger this. I'm uploading same file two times however with different title as below.

    ftpClient.storeFile(fileDir+"//"+"actualFileName", inputStream));
    ftpClient.storeFile(fileDir+"//"+"differentFileName", inputStream));

I suppose it is the second file that eventually ends up empty. You need to recreate the inputStream for that second update (per DRCB's comment), otherwise it will likely be empty (it has got consumed through the first upload).

A remark: "//" appears a little strange, shouldn't it's "/"?

You repeat storeFile with similar inputStream, that will happen to be read towards the finish. InputStream includes a read position. Consequently the 2nd file is really empty. Also make sure you close() the input stream not to lose file handles.