So Steam installed the new flap fix update after I adjusted my flaps to fix the issue caused from the England scenery update aka: update3.
After the update was installed, I went to go fly the Cessna Longitude, because I know I didn't change those flap settings manually. I also flew the Cessna 152 that I did change the settings on previously. I almost feel like the Longitude was a bit spongier then I remember, but it could just be me.
However I did notice that when you go into the aircraft config file even after the update, the flap settings I had changed were at the same values I had changed them too, to compensate for what happened with update 3. So if anyone else changed them and then installs the update remember to change them all back afterwards.