Some of the things that MAY be relevant:
Flaps increase directional stability, which generally helps for VMCA, but also sideforce, which hurts.
Flaps may or may not increase dihedral effect and roll power, depending on where the roll control surfaces are, which may help or hinder if VMCA is near the roll control limit.
Flaps (of course) reduce AoA for a fixed speed, which may make the rudder more powerful, helping VMCA
Flaps reduce load on the mainwheels at a given speed, which might hurt VMCG.
Obviously, on a type with powered lift (like a dash 8) flaps can make a big change to all the aerodynamics.
How each of those (and other) effects interact will be very dependent on the specifics of a type design. There's no simple relationship you can reliably state.