If your opponent targets “Machina Fortress” with an Effect Monster’s effect, then Chains with “Enemy Controller” to take control of “Machina Fortress,” you will not discard a card from your opponent’s hand because it is no longer being targeted by an opponent’s effect.
If you have more than 1 “Machina Fortress” on the field and your opponent targets them all, you will discard 1 card from your opponent’s hand for each “Machina Fortress” targeted.
When this card is targeted by an opponent’s Effect Monster’s effect, you look at the opponent’s hand and discard 1 card from it immediately before resolving the effect of the Effect Monster. For example, if “Machina Fortress” is targeted by your opponent’s “Brionac, Dragon of the Ice Barrier” you first decide whether or not you want to Chain any effects. Then, when you go to resolve the effect of Brionac, first look at your opponent’s hand and discard 1 card from it. Finally, resolve Brionac’s effect and return “Machina Fortress” to your hand.
If "Machina Fortress" is targeted by an opponent's Effect Monster's effect, then you check your opponent's hand and discard one card when the opponent's Effect Monster's effect resolves, before doing anything else.