We went through a similar situation and called. They said that they do not take schedule changes but suggested that we e-mail admissions so that when the transcript arrives and the classes are different, they would know why. We e-mailed and received an e-mail reply back from the admissions dept stating our particular change in senior year classes wouldn’t affect admissions in our situation.
As far as how it will affect you, I don’t work in admissions. I can only tell you what the admissions people told us when we called and e-mailed.
Why do you say that it is too late to notify the school(s) of your schedule change?