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If I have Emergency Defense Field and Recon System attached to my character, and its attacked, can I choose which battle card to scrap (Recon System) after both players cards are flipped, to try and trigger Energy Defense Field?

Yes, you can choose which card to scrap. The attacker always flips first, then the defender. Since youre defending, youll know what the attacker flipped when you have to decide for Recon System.
Source: Wizards of the Coast (2019-06-28)    【Link to Ruling】
Tags: Recon System