Why does my professor use both the upper, and the lower, case literal of a letter to symbolize the same concept?
Of course, there is a convention. In physics $E$ usually stands for energy, $e$ for elementary charge. You professor is inconsistent, to say the least. In my opinion using lower case $e$ for anything rather than for elementary charge is wrong by itself, and using it for energy is simply ridiculous. Besides, I don't see any reason for doing so.

P.S. During my university years I had a professor who randomly picked letters for physical quantities every lecture. :D Today I think of it with a smile, but at that time I hated both his lectures and him personally.