How did Nidhogg lost

[Yukiko]

Because Nidhog was just a Shadow and not in his "real" Body.
To create a physical Body out of Willpower to fight us, it cost him a lot of Energy and that energy he will miss in the fight.
In add he had to overpower the "will" of his host, again he lose some energy.

About our past win against him:
He lost both of his eyes what should have been his death.
He just hadnt his original physical power - you can compare it with permanent healing against cell degeneration.
In add Hraesvelgr does not agree with what Nidhogg is doing and you can guess the borrowed Eye from Hraesvelgr resists the hatred from Nidhogg to some degree.