Flood had made the No.10 shirt his own in recent years and appeared to come into his own during the RBS Six Nations.
However Wilkinson appeared to move above him in the pecking order during the warm-up games - culminating in the Toulon star starting against the Pumas.
Wilkinson, though, endured a miserable day with the boot, while England struggled for momentum.
Flood is now set to get his chance in Sunday's clash with Georgia and he has a point to prove.
"It was really frustrating not to be part of the first win but you get over it pretty quickly and realise it's a massive squad effort," Flood said.
"It is difficult but you take it on the chin. In coming weeks the squad is going to be important.
"You can't let it knock you. All I can do is go out there and try to prove them wrong on the decision they're making. You hope you get the chance and make an impact, put your hand up when you get an opportunity.
"They haven't said 'You're second fiddle or whatever', each week is selected on form more than anything else."
Flood grew up playing with Wilkinson at Newcastle and he claims they are the only two people who seem not to be fixated with their battle for the No. 10 jersey.
"You get asked it every other day. Even my mum asks me the same questions," Flood added. "We get on better than most people think.
"(At Newcastle) I never saw it as a competition but as a chance to learn from an outstanding player. When you're 18 or so and you see who's on top of the world, it's amazing to be there.
"It's a talking point outside the squad but between me and Jonny there's no big high five or handshake of congratulations about getting the start.
"It's just down to business."
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