The project I'm working on is about replacing a USB flash drive with a network based USB drive. The requirements of the proposed solution is listed below.
Use of RFID card
Mount remote server directory to local USB host based on selected user
Operate via Wifi and etc
And my planned solution begins with compiling the LUFA MassStorage demo with the Arduino Leonardo board settings. I have managed to do this part. Then I'm planning to use the ISP protocol for AVR programming to upload this .hex file to the Leonardo with the help of Arduino Uno. Is it possible to further program the Leonardo after doing the above step? If yes what are the steps I should take?
Whether it can be reprogrammed over USB isn't immediately clear - though it claims to have a USB bootloader for mass storage device. You'd need to study the documentation to determine if this would be appropriate for your purposes.
That said - you are going to be very disappointed with the performance of this if you can make it work at all. Shuffling large amounts of data is not something the 32u4 (or any AVR) is well suited for. Something like this really calls for a beefier (computationally) microcontroller. I haven't done anything like this, but I've heard the Teensy suggested for applications like this. The STM32 line might also be appropriate.