Can I use a flour based thickening agent for home made gummies? I'm using the same measurements?

Same as what? If you have a recipe, you follow the recipe. If you don't have a recipe, you go find one.

Gummy candy uses gelatin, not flour. Flour is opaque, gummies are translucent.

Here is a recipe. I do not understand why you want to use flour in such a simple recipe:
abeautifulmess.com/2015/04/make-your-own-gummy-candy.html