Lerager Meridian flip - when you are imaging a target and that target passes the meridian, the mount will do a flip in order to continue tracking the target.
Darks have nothing to do with Meridian Flip - they will always be the same regardless the orientation of the camera/scope.
Mixing darks from AA with other darks is not a good idea; I had horrible results when I tried to stack images from StellarMate with darks from AA because of different offset values. My advice, take enough darks at different settings and make a library.