Finally my visa has been approved today. Status got updated on the CEAC website for the first time after interview on 11th July after 58 days (still said administrative processing). Same day, I got a call from the embassy asking me to go there on the 12th. They didn't reveal if my visa was approved on the phone but I called the DOS and they said that they could see "ready to issue" status on their side. I went to the embassy on the 12th morning and the consular told me that my visa is approved. I paid the fees and got out happy! I am collecting my passport the same day in the afternoon!

The consular revealed to me that my case was kind of lost and he apologized to me for the delay. I guess my advisor's email woke them up and had them looking for my case! So, if anybody in similar situation, have your advisor/supervisor contact the consulate. It might  or might nor work, but i think it's worth trying just in case your case is lost or stuck like mine.

Thanks to everyone for your input and for sharing your cases. It was one of the most stressful times in my life, and I hope people will at least learn from my experience and take precaution if they are coming to Nepal for visa renewal.