It isn't harmful to get baking flour in your eyes. Because there are toxins in baking flour, so you don't need to worry too much. What you should do is to wash your eyes careful to get flour out and then go to ophthalmologic hospital to check your eyes in case of infection.
It is really painful when the bit of baking flour coming into your eyes. You'd better use the clean water to wash it out. Just use the clean water and a clean cloth to dry it. It will be OK. If you are not at assured, you could go to the hospital to take the professional eye washing.
I am sorry to heard that your eyes get baking flour. You must use clean water to flush your eyes immediately. Or you can use your eye drops to flush the backing flour out of your eyes. Usually, it will be ok after flush the baking four out of your eyes. If it is not work, you'd better see a doctor. Hope this can help you.