Hi. My league is a 9 hole league that plays both 9's on our course.
I've set up each 9 as a separate course but neglected to put in
different USGA amd slope ratings for the more difficult side.
We've already played 4 rounds. If I change the slope and USGA rating now, will it affect the handicap used for previous rounds?
That's correct; it will affect previous rounds, unless you create a new course with the correct handicaps and use the new course in your schedule for the rest of your season.