You didn't tell us what cookie you're baking, so here goes.
Don't know if this is right or not. Hopefully you will get a bump with someone more qualified answering the question.
Egg yolks give you fat and flavor.
Egg whites give you height and lift.
The above statements depend on how you use them.
Personally, since the stuff is already made I would bake it all off. You might have created the favorite family cookie.
There are bigger experts in the cookie dept. here than myself, but the only time my cookies became tough was because I over mixed the whole shabang!
The spritz cookie recipe I have uses yolks only. I was looking the other night for some different flavors of them and did find some that used whole eggs. So I guess it all depends on the recipe.
I'd bake what you have, and see what happens. You can't take the white out at this point, but I wouldn't throw it all out. You never know you may have improved on the recipe. 
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