3.36.0 is ancient. You should update to a recent version.
I am amazed that this works as well as it does.
I believe the other user who suggested this path was taking the geometry to CAD, fixing any issues there, and proceeding.
OpenVSP is being forced to do some weird things to loft the surfaces through that rapid transition. The mesher is then doing the best it can with an ugly surface.
I don't think you are going to have a great deal of success with this.
However, your best bet will be to break the main wing into three segments -- one before the flap, one traversing the flap, one outboard of the flap.
This will fix the problems with the abrupt transition between sections, but it will introduce its own problems with trying to make tiny perfect intersections between the wing sections. I'm not sure what you'll be able to do there -- particularly in an OpenVSP only workflow. This is another approach that may work best with CAD post processing involved.
Rob