@lookingforward in OP’s defense, it’s the default assumption for many people who follow the A-level system that unis only care about GCSE/AS/A level grades, because that’s how it works for UK unis/unis in countries that follow A-level system - school transcript is pretty much irrelevant to oxbridge, for example. Internationals probably decide later (say in junior year) that they’re interested in applying to US colleges and do their research, and by then it may be too late to save your transcript.
That said, I stand by my personal experience from my country - top schools seldom admit those with questionable transcripts regardless of final A level grades. OP might want to ask any seniors from his/her school who got into top US colleges what their transcripts were like, and that might give an indication if top colleges are familiar with this situation and are willing to overlook it.