I would go with something more like:
Dear Whoever,
I hope that this message finds you well. While I understand that the application season is a very busy time for your office, I am wondering if you might be able to honor a small request? In light of the requirement of two letters of recommendation from science faculty, I would like to change the letters of recommendation assigned to my AMCAS application to ensure that the letter written by Dr. X is evaluated, as opposed to the letter written by Mr. Y. Thank you for your time, I greatly appreciate it.
Sincerely,
st.jude