I should qualify my previous statement by pointing out that I have never actually had a tree die from fb canker. What happens is I try to scrape it out leaving the leader in tact. It will look ok for a while even up to a year, then start to come back with oozing etc. So I cut my losses by cutting the tree down and starting over. So maybe I’d still have my original trees if I’d left them alone who knows.
You could cut back to your lowest branch and have that serve as your refuge for possibly contaminated scion. That way if new grafts start to show fb you can then cut that branch or entire leader and still have a single leader tree. I think your scion will be ok if you can stay some distance from the canker. I’d recommend grafting in the evening and ideally wait for some cloudy days if that is even possible in your location
Or do like Scott and roll the dice. He has way more experience than I do. Either way I’d be curious how it turns out. This situation has happened to every apple tree I have planted this far, grrr.