Has anyone looked into how much protein is lost during the bread baking process?
It depends on your process. It could be 25grams of protein per minute.
... and 50g for twice as much dough! ;)
Oh, wait, I'd still like to call "Bu... But could you please explain further!".
I might be wrong, but I believe that most of the processes, like proteolysis, that destroy protein structures, break the proteins down or transform them, but the parts can still be used as protein (or amino acid) source by the body when digested.