The last batch of challah (bread) that we made had a very chalky undertone and aftertaste. This time, the dough has a faint smell of the chalk (we didn't bake it yet). The flour has no odor and was kept in the freezer until now, and the yeast is not expired and didn't smell off. Could it be the addition of honey to the dough? Any ideas?
It is most likely that the smell is originating from the flour and the smell has been released during your dough making process. Limestone is added to flour to help us maintain our calcium levels and reduce the risk of bone diseases Limestone And Its Everyday Usage
Chalk is chiefly composed of limestone (calcium carbonate).
Limestone when "purified", it is added to bread and cereals as a source of calcium. wikipedia.
Anyway don't worry it is quite safe to eat chalk/limestone. Interestingly though seldom mentioned on western web sites, Lime (calcium oxide) provides some control over insects found in grains etc. This subject relating to the use of inert dusts is disgussed in the scientific paper "Ecologially safe alternative for the control of stored-product insects".
These materials have been shown to control a variety of common storage insect pests. They are most effective in conditions of low humidity because they induce mortality by causing desiccation; water is lost because the dusts remove the waxy layer of the cuticle of the exoskeleton by adsorption. These materials are most effective when applied as dusts
However if you wish to read this paper, you need to buy it; But it is very briefly refered to here Control Strategies of Stored Product Pests