Maybe the Aevis can sense the immense sadness in Francel as he approaches and they can relate, due to sadness being a driving force for Nidhogg's rage and then because they're no longer under his thrall they don't have that rage overshadowing all other emotion and so don't feel as though they should be aggressive towards him.

Meanwhile, they'll attack the WoL because the last moments of Nidhogg's life would have been pure malice directed towards them which might still linger.

#headcannon