You would have to use materials to level up both of your duplicates.
They'll ending up getting merged together eventually, so I would count it as an opportunity loss of those materials.
You always wanna prioritize leveling characters you think you'll keep around the longest.
You always wanna look at the event running that week and what character will be replaced when you receive them.
Decide which of your team members is "on death row" and try to hold off on using stuff to level them if possible.
You'll reach a point in the game when you are scrounging to level your good characters and you'll be thinking to yourself "why did I waste all those good red manyus leveling that duplicate character?!"