As you stop the lens down to smaller apertures, your viewfinder will dim down and the light reaching the Focus Confirmation sensor will be reduced in the same manner... At some point FC will not work. Depending upon whether shooting at high Noon on a bright sunny day or in low light, you might be able to use FC to f8, or even f11. But it will fail sooner in lower light situations.
Although this is true, it usually doesn't matter. The usual procedure for shooting manual lenses on dSLRs is to focus and compose wide open, then stop down and meter, then take the picture. This way focusing is easier and at full brightness. The AF confirm chip will then work fine regardless if you shoot at f/6.3 or f/32 since you have already focused before stopping down. Some older lenses even have an open/close ring separate from the aperture preset ring to make this process even easier.

