I think you might need to elaborate on what you mean. Are you dredging the chicken in soy flour before you pan fry it? Are you using flour in a roux to thicken your Marsala Sauce?
If you don't dredge the chicken or use a roux you should be able to make it without flour entirely.
Soy flour as a substitute for white flour is a step in the right direction to healthier eating. Soy flour has 3 g of protein in just 1 tbsp. wolframalpha.com/input/?i=soy+flour Keep in mind, that a well balanced diet is not just about eliminating a particular group of foods, but about eating a variety of foods that are nutritionally dense.
Whole grain foods are a good part of a balanced diet.
The substitutes for making a low-carb version of Chicken Marsala are : Mascarpone instead of Cream, Low-carb substitutes for high-carb foods such as breads, pasta, candy Dry Vermouth for the Marsala.
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