I didn't realize that CMDelete.exe was a program that came with Control Manager, but I have found it now. However, it still didn't seem to clear the calibration and it's still using both axes. I had already downloaded and ran Control Manager, though. That was actually where the problem started as it only began using both axes after I ran the Control Manager calibration. I was just trying to get rid of a very slight drift to the right, but it was not using both axes at that time and still worked more than good enough to fly. Again, it was only immediately after using Control Manager that it began to use both axes.
I'm hoping for some way to completely reset the calibration data. Is there another way besides using CMDelete.exe or ClrCalib.exe to do so? Seems like there should be a registry in Windows I should remove or something like that, but I can't find anything that would do it.