My first thought was that you could just flash the kernel. That would not have touched your data. Or a flash of rootfs.. that would need you to reinstall your programs but your personal files would still be there.

However.. when it takes you so far as the desktop. My guess is that there are some config or personal file that makes it reboot. It might still be enough to do the above. If it some process that starts late or it disables the program causing the problem. But when you have made the back up i would still make a complete reflash of both Combine (rootfs) and Vanilla (eMMC).