Restart the software and it should prompt to restore the settings.
I just bought and DL'd the FoCal Pro software a few hours ago and started using it on one of my 5DMKII's and my 5DMKIII. It's pretty slick on the MKII because its fully automatic, but on the MKIII you have to enter the AFMA values manually into the camera because they still can't gain FULL control over the camera.(the software does prompt you when to enter and waits on you). I have had a few issues with it locking up/hanging up on both bodies, but it may because there isn't a Mac version yet and I'm running it on Windows 7 via Parallels. Never rule Windows out as the cause of a problem . While attempting to MA the long end of my 24-105 on my MKIII it looked to be about 3/4 done and just hung in what appeared to be a loop of analyzing and acquiring data/images, even though it wasn't taking any more pictures. I had to force quit the software. But the sessions with my 70-200v2 and 100mm Macro on the MKII went off without a hitch. One thing to be aware of(and this could be user error, I haven't read all the way through the manuals), is that the software leaves your camera in the state that IT did the testing, i.e: mirror lock-up on, picture style changed, ISO changed, metering changed, focus, etc.
Hopefully tomorrow I will be able to finish all the lenses on all the bodies and see what the real world results are. Thank goodness there's software now, because doing this all manually with just a target and having to look at all the images yourself, with even just one or two lenses, would be insanely tedious. It felt bad enough having to just enter the software prompted AFMA values into the MKIII by hand after watFching it with the MKII on auto-pilot .