Will my progress as john transfer back to arthur missions?

I am currently attempting to 100% the game, and I plan to do the story missions last as by that point I figure i'd have all the boosts (from trinkets, items etc.) and all the weapons, outfits, and items I unlocked playing as john, to make the gold medals easier. But I realized I don't really know if theyll transfer over. Will they, and if not, do I need to buy everything and unlock everything all over again?