Negi is the bastard child of Nagi and Eva. Nagi turned Eva into a little kid because he got her pregnant and she was chasing him to raise the child. Unfortunately she was still able to give birth as a 10-year-old and she left the baby on Nagi's doorstep. Then Nagi's like WTF and disappears, pretending to be dead.
Later he reappears and turns the aging Asuna into a kid again because he always wanted to have sex with a delicious loli and couldn't do it with chibi Eva because she was already pregnant (not to mention furious with him). He wipes Asuna's memory when he's done which is why Asuna has memory loss. He makes a deal with Konoka's grandpa to let Asuna have a normal life at Mahora in exchange for keeping the molestation of his granddaughter a secret.
And with that all your questions are answered.