The moral of the story? You cannot trust Comodo to be able to upgrade anymore. Download the installer, uninstall the old version and install the new one.
This is a good idea with every program, not just Comodo. Before uninstalling take screenshots of all configuration windows and in the new version re-do the settings manually. Although it sounds inefficient, sticking to this philosophy will save you lots of grief and some early grey hair.
Another idea you should consider is to forget about restore points, they are unreliable. I turned off that Microsoft creation years ago, it's just a waste of disk space. Instead, find a reliable disk imaging program. I use Acronis True Image Echo Workstation installed as a BartPE plugin on the bootable flash drive, it's a bullet proof solution (TrueImage wouldn't work under Windows XP on my system that's why I put it on BartPE media).
After my latest Comodo upgrade from v2.4 to v3.13 and trying out some other applications, I wiped out and then restored partition C three or four times. All it takes is about 3 minutes to restore drive C from the disk image.