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Let’s say I flip 3 battle cards (the normal 2 + 1 for Recon System) and there’s a white battle icon there. Do I scrap one for Recon System’s effect immediately or do I flip the 2 extra cards?

Flip the extra cards first, then choose one of the cards you flipped and scrap it.Note that this was overruled inRoundup 2019-03-08 below.
Source: Wizards of the Coast (2019-03-01)    【Link to Ruling】
Tags: Recon System