Yes, as clearly indicated in the prominent header in that file:
###############################################################################
# FILE AUTOMATICALLY OVERWRITTEN BY PI-HOLE INSTALL/UPDATE PROCEDURE. #
# ANY CHANGES MADE TO THIS FILE AFTER INSTALL WILL BE LOST ON THE NEXT UPDATE #
# #
# CHANGES SHOULD BE MADE IN A SEPARATE CONFIG FILE: #
# /etc/lighttpd/external.conf #
###############################################################################
Changes to the lighttpd port should be made in the external.conf file, which is not subject to be overwritten by a Pi-hole repair or update.