It would depend on your assessment rank. If you were ranked first it would not affect it at all- you would keep your high marks. But the lower your rank the more likely it is that your school would have dragged you down.
If you were ranked 10th out of 50 your HSC mark would be the average of your exam mark and the 10th highest exam mark from your school.
But if you were in the top 5 it would hardly lower the mark.
But once you have your HSC mark the UAI is calculated from that mark and UAC doesn't look at what school you went to or how it performed as a whole.