" Does the CMOS Battery have any effect..."
I guess you mean the button back-up battery? If so the 1D Mk II will work with or without that battery. All it does is keep the time and date. Unfortunately anything made by the hand of man can and will eventually fail. You need to try another lens or two. It is the lens that focuses not the camera. However, the camera has to tell the lens to focus.
Other than the AF, it is working OK?
I have tried all my lenses even on manual focus sharp in viewfinder photo not in focus like i said t was fine the day before .I know on the 7D MK1 if you took the CMOS battery out it reset the camera so it would focus ? The conacts are clean on camera and lenses ?.
Does that camera have a "live view" mode? If so, and if the problem doesn't occur in live view, there may be something wrong with the viewfinder's AF. The two mechanisms are almost totally separate.
Just a thought - could it be an accidental diopter adjustment?
If you're using manual focus, and your images look in focus through the viewfinder, but they're not in focus when you review them, it's my experience that the diopter is maladjusted.
Make sure you have a lens that's verified as working, and in Auto Focus, and put the camera in an "Automatic" mode. Do step 1 below. Focus on something (wait for the confirmation beep), and then do step 2 below.