Hi,
Yes, cropping the footage might introduce some discrepancies. Anyway, depending on your data, the impact may be limited.
Principal point (the projection of the camera center on the image):
The problem would be that the principal point might change. So, either you now where your new principal point is and you enter it in your camera settings, or you manage to keep your new principal point at the center.
Focal length:
The focal length is usually defined on the uncropped footage. So any fixed focal length you provide should be adjusted. If you let the software automatically adjust the focal length, and you use the same cropped footage within the composition package, it should be ok.
Hope this helps.