Activision has placed a secret program hidden on the 3DS version of Skylanders that can repair the majority of Skylander figure problems.
If your Skylander is no longer being registered on the console versions Wendel can repair them. Place them on the Portal of Power and go up to him with the broken Skylander he will say the Skylander currently placed on the Portal is corrupt and will ask if you would like to repair it. Accept and he will fix your Skylander. On a side note, it will reset your Skylander progress, but at least it will be fixed.