i could be wrong, but i don't think the game saves independent versions of characters.
For example, if he is player number 1, the game is going to load his versions of both characters, and then you will take over one of them. But it is not possible to 'merge' two characters from two different games in the same play-through.
Allowing such would cause a conflict in the crystals, like you described. Which is probably why the designers didn't allow it. i wished they would have created a version that did, tho. With a lot more weapons and items.