Morgan Lofting, who lent her voice to the Baroness, thought little of how DIC interpreted G.I. Joe; in fact, she refers to their series as "the D*** version".
Gnawgahyde and Metal Head are the main field commanders under the control of either Cobra Commander himself or Destro. Replacing the Dreadnoks as the main mooks.
Storm Shadow left Cobra and joined GI JOE
Originally, Tomax and Xamot were supposed to lead the remnants of Corba as the Coil and be in competition with the newly solo Dreadnoks all while fighting GI Joe. Cobra Commander would be restored and work from the shadows to regain his lost power and dominate Cobra once more.
Extensive Enterprises shutdown by the time of the series. Possibly Tomax and Xamot cut their ties with Cobra and started a new business for a clean start away from them and GI JOE.