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I wouldn't use self rise flour, it has baking powder in it. That said I have never tried it so don't know how it will work. Do you have cornstarch? Maybe you could use that.
If you use the self rising flour, it might fizz up from the leavener, but that should cook off. It might introduce an off taste, though, and both baking powder and salt added to the flour would increase the sodium, so you'd have to be cautious not to over salt.
Your milk will most likely curdle as well. Self raising flour really isn't appropriate for bechamel.
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