I have Franklin left and thats it, my opponent has feral Sabertooth. 11/4. He attacks Franklin. Franky runs away to the bottom of my deck. Do I still take breakthrough or stun damage? Or does Franks expedious retreat negate the attack?

If the defender is removed from combat, then the attacker is readied and has the option to declare a new attack.

Franklin runs away, but because there is no longer a defender for the 'Tooth, he can make a different attack.