By that, if you mean completely disabled and rendered unuseable, I'd have to say no. Unless a feature was rendering motherboard(s) inoperable, I can't imagine them disabling a BIOS feature completely. If anything, it might have its default status altered, like being Disabled by default rather than Enabled, but that's as far as I see it going.
Also, as for your concerns about the overclocking settings, just note the few settings that are relevant, such as CPU Settings, memory timings, FSB adjustments, voltage tweaks and PCI clock settings (don't know if it applies to newer PCI-x boards though). That really won't cover everthing, but it just occured to me that if you have a cheap digital camera, just take snapshots of each respective BIOS screen so that you can review them later on. You might end up with a couple dozen photos, but it can be critical to getting your rig back to what you had before.