Short of sandblasting or hand wet-sanding, no, cured clear coat will not come off easily. If it is shellac, mineral spirits MAY work, but will risk getting that on rubber hoses or plastic that may degrade them significantly.
Depending on the severity of flaking on which engine parts (intake manifold or valve covers), it may necessitate removal of these items from the engine to properly and completely "clean" them of whatever coating is now degraded to the point as you have examined.
Are you sure it`s not aftermarket undercoating that may have been dealer-applied??? This will also flake off when a vehicle has seen many years of service. You also failed to mention the car`s manufacturer, vehicle model, and model year it was made. Is the engine a V8 or a 4-cylinder? Not that it matters, UNLESS you are going to remove these engine parts yourself. If it`s a Jaguar, Mercedes, or other hi-end car, you may feel slightly intimidated, depending on your mechanical prowess and experience.