The AF isn't lost it just might not work as expected; that is, keeping the grain sharp as the head is moved. The Schneider optic I swapped the original lens for is a 40mm so the AF is still pretty close. I'm sure there are differences, though, because this enlarger was engineered for the Leitz 40mm lens. Anyway, in my testing even using the original lens I found the AF to be very slightly off. Of course, this could be that the AF was malfunctioning slightly on my unit but it didn't concern me because focussing with that helical mount is absolute precision compared to, say, my Beseler 45! Plus, I've been using a grain magnifier for so long I'd be lost without it!
One thing I still enjoy about the AF system is that the image stays relatively in focus as the head is moved. To me, this makes it much easier and faster to get actual printing.
I've never used the color head for VC printing...note to darkroom mole: try the friggin color head!