In Asylum of the Daleks, Clara did wipe all memory of the Doctor from the Daleks.
But in The Time of the Doctor, he shows up on a Dalek ship holding the eye-stalk of a destroyed Dalek.
When they saw that, they attacked him as a normal adversary. Watch the episode, and you'll see that they just screech their usual EXTERMINATE without mentioning The Doctor.
So, the Daleks' didn't remember that he's their eternal enemy The Doctor. He showed up with a eye-stalk and said
'I bring proof of courage and comradeship. What is this ship and why are you here? Identify yourselves by species and planet of origin.'
So they attacked him like they would anyone else.
Also as @Amy mentions:
When the Daleks eventually attacked the Church of the Papal Mainframe, they harvested data about The Doctor from Tasha Lem's Cadaver. But this was after the scene when he walks in with a Dalek eye-stalk, at which point they had not known who he was.