There is a good story about Ngawang Khedrup, that once when he was studying in Khasa, he was falsely accused of breaking his vows. Ngawang Khedrup consulted the Nechung Oracle for a solution but was told instead that only Dorje Shugden can tell between what is the truth and what isn't on this matter. So on Nechung's advice, Ngawang Khedrup consulted Dorje Shugden and the problem was resolved soon after.
Nechung has always known who Dorje Shugden really is and it was Nechung who reminded Tulku Drakpa Gyaltsen(TDG) of his oath to be the Uncommon Protector, made in TDG's previous reincarnation as Duldzin Drakpa. And again in the case of Ngawang Khedrup, Nechung demonstrated trust and confidence in Dorje Shugden.
If Nechung has such faith in Dorje Shugden and HHDL has a close relationship of trust and friendship with Nechung, it doesn't add up that HHDL would have adverse views towards Dorje Shugden. HHDL has this to say about Nechung:
"Yet we are very close, friends almost. When I was small, it was touching. Nechung liked me a lot and always took great care of me. For example, if he noticed that I had dressed carelessly or improperly, he would come over and rearrange my shirt, adjust my robe and so on. Nechung has always shown respect for me"
It does make sense for Nechung who apparently likes HHDL so much to have faith in Dorje Shugden if indeed Dorje Shugden is harmful to HHDL and also to Tibet especially if Nechung, in the words of HHDL has the same responsibility to Tibet as HHDL.