Generally a high fiber flour is also high in protein so, to some extent they are interchangeable.  However, some of the high fiber flours like Montina and teff have distinctive flavors that should not be used to prepare delicate cookie recipes, cakes and cupcakes.
They should be reserved for bread baking and recipes that call for molasses, honey or brown sugar and warm spices.  The high protein flours such as sorghum and chickpea flour are great as part of a blend for pizza and pie crust where the dough is rolled out thin and
the structure needs to hold together.