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In a recent match in Teambuilder I played against a Nidalee. When she threw her spear, Yasuo would take damage even though he had max flow and the shield wouldn't even activate afterwards. Also, his flowbar is depleted instantly, as well. I've looked at both the descriptions of Nid's spear and Yasuo's passive and I see no reason why the spear should be an exempt from the passive shield.
I'm sorry that I don't have physical proof, but please believe me on this one.