Better to just avoid having duplicates of any type of weapon, they might not be needed now but they might be essential in near future just like Miaki etc. I would only consider duplicating if it's L/S chest and nothing else. Always refer to altema which is a lot more accurate in terms of drops...
How do you manage to have 9000 Kt Shadow without consuming making your Murasame Starchart negative? Are these all farmed from chest? I don't think there's a way to remove negative from bonfire trade unless you're familiar with manual inspection with GG.