Yeah, Kali Yuga's eff states: "other cards and their effects cannot be activated on the field, and other cards' effects on the field are negated."
Meanwhile, Madolches go, "If this card in your possession is destroyed by your opponent's card (by battle or card effect) and sent to your Graveyard: Shuffle this card into the Deck."
By this reasoning, Madolches have to be in the Graveyard to activate this eff. Kali Yuga's eff only works on things on the field, so the Madolches' effect resolves normally.
Meanwhile, Madolches go, "If this card in your possession is destroyed by your opponent's card (by battle or card effect) and sent to your Graveyard: Shuffle this card into the Deck."
By this reasoning, Madolches have to be in the Graveyard to activate this eff. Kali Yuga's eff only works on things on the field, so the Madolches' effect resolves normally.