the condition of the figure shouldnt affect the nfc part that gets scanned in. im not really sure how that could be damaged from inside the amiibo base unless you tried taking it apart?
edit: sometimes i get bad amiibo readings though, and it does say something like "this amiibo cannot be used" but they're not broken, it was just a bad contact with the reader and trying again in a different position usually works. restarting the software might be helpful too