In Nepali NGO, they look investors from Expats. The government has limited foreigners to work and visa processing is a bit problematic. I have a friend from Britain who is working in Nepal for Ramechhap District. She too had visa processing problem due to which she has to return back to England to correct it.
So, I am not sure if it can be good for your plans. But I will highly encourage you to continue working in India. I believe soon Nepal Government will amend the rules for expats.
Best wishes.