I used a brake type hone withh a flexible shaft when I worked on Seawebs fork.
It was a combo of the aftermarket fork being a bit oversize and scoring, in the bore. It took quite a while to get some clearance, slow going.
I would not worry to much about a few scratches but check tube for damage and give it a light hone to remove highest spots. Check tube size, what is snug for aftermarket may run nicely with a stock tube..