Gabe is correct that they can't be directly negated because they're in the deck, and thus not targetable.
What I am unsure of is if they can be indirectly negated by negating the D3. #EDIT# After some research and consultation, I have come to the conclusion that Gabe is correct that it cannot be negated after exchanging, no way, no how.
If they used something like Magnificat to set-aside your EC (Which is what I think you meant) Then yes, you have initiative to negate, if they played something like First Fruits (Like Gabe thought you meant) then you do not have initiative.
Also important to note here, is that Consider the Lillies is worded with Search language, so I believe that the card goes to hand, not battle, so if they have some numbers, you may actually have had initiative before they played the card.
