You don't say if it's an upward or downward bow -- but yes, it'll act the same as a warp. Very roughly, it's the amount that the TE is bowed up or down that matters, whether it's the TE of a flap or the TE of an un-flapped wing.
If it's not a super-rigid carbon fiber flap, you should be able to correct it with heat -- dry iron if it's 'coat, moist heat if it's silkspan & dope.