What do you think? If both Flaps are connected via Y-cable and thus receiving the same signal, what do you think your elektronic and software can do to have them moving in different directions? Right, this can only be done mechanical and you need to uninstall a servo and put it back in reverse.
Having this in mind, it is clear that you are most probably a very beginner. I highly recommend to go for local assistance. I am sure there are more problems in your setup and you dont want the risk of loosing the plane.