Today I removed my mudflaps after a bit of indecision. I did a bit of CFD to test, and came up with these results.
The flow lines are a bit hit and miss - there is definitely much less turbulence (and drag) inside the wheel arch but the air is more turbulent behind the wheel now. However, the mudflaps appear to be creating downforce - check out the larger number of lines heading down to the floor with the mudguards on.
*** images are thumbnails which can be clicked for large version ***
Now when we look at the "Cut Profile" through the mudflap section - this is more like it. Red areas are slowed down air i.e. drag. and there are a lot more of them. This is the view which made me ditch them from the car.