It's my understanding that Enhanced Flailmanship while restricted to flails or any kind of swinging weaponry (eg. a ball and chain, or a bola), is mainly composed of a 'striking head attached to a handle by a flexible rope, strap, or chain'.
Whereas Flexible Weapon Proficiency refers to any weapon that is flexible in nature. A lasso or simple wire would fall under this category, but not Enhanced Flailmanship.
Enhanced Flailmanship could be a sub-category of Flexible Weapon Proficiency, while the reverse wouldn't be true.