Does flour as thickener get rancid?

They do not recommend using flour as a thickener when canning items as a rule- not because it gets rancid, but because it can make it difficult for the heat to completely penetrate the product during the canning process. The temperatures for canning would prevent anything fermenting in a properly heated and sealed jar. However, there are a few exceptions to the rule and there are professionally developed and approved canning recipes that do use a small amount of flour as a thickener. Otherwise the only approved thickener is a product called Clear Gel, which is a modified form of corn starch. Ball has a recipe for an Oriental style hot sauce that does call for a few tablespoons of flour, though- so that's something to look at and consider. Amounts you will use are important, as well as how thick the sauce will be when it goes in the jar. I expect you are thinking of a sauce that is still fluid. Perhaps you could also consider reducing the amount of liquid to start with, or cooking it down to concentrate it further before canning, as other options in lieu of either the Clear Jel or flour.