Our GC does not read the LoRs from teachers, so I don’t know which was “better.” I was just ideally wanting the science one to be sent since engineering is the intended program.
I got an update that I had been given the wrong info yesterday and in fact any college that allowed two recs was sent both LoRs. Only one school accepted a maximum of one LoR. So I got alarmed about nothing, except that (in my defense) the initial reply I got was not reassuring. Luckily that was not correct. Thanks everyone for chiming in. I learned a few things about Naviance!