It depends on your claims that end up being granted. You can file an application with both claims to the component and to claims to the modified whole system. It may be that your component is a particularly shaped cam and it makes the whole device unique. But the cam itself, sitting on a shelf, out of context, might not be new. If you have a claim to the shape of the cam then any previous cam of that shape for whatever purpose would show your cam not to be new.
Also, the part may cause a behavior of the whole machine to be a certain way. If you claim - for example - a windshield wiper with intermittent operation then there may be an existing system that does not use your part but has intermittent operation. That claim would not be to a novel system. Each claim is looked at for novelty and non-obviousness on its own.
It may also be that the examiner sees this as an application for two different inventions and requires you to chose one to pursue in the application. The other could be pursued in a divisional application.