I'm pretty sure Tabuu (the program) can do this, but it won't be one slot, if that's what you want. It's not really "swapping" it, per se, but rather you're just telling the game to look at this bone in place of that.
It's more useful for model swaps, which will make the TransN act like a TransN, regardless of the bone indexof the original model or the swapped model.
If you were to just randomly change the bone index on a single character, I'm pretty sure the animations would screw up completely, or the game would just freeze up.I would go
here if you have any questions.