I'm pretty sure cloning the Togepi won't change whether or not you can trade it. There were no sensors to check for hacked pokemon/glitched pokemon back in Gen 3. Those kinda pokemon didn't start getting flagged until Gen 4. Forgive me if I'm wrong, I would've tried simulating this because my Togepi has not been traded for the Elekid to help answer this for you, but sadly my pokemon Emerald game died on me before I could even start trading between Emerald and Gale of Darkness.