What happens when you divine a legacy unique that has a mod that doesn't exist anymore?

The short answer is that's not something you can possibly do - if the mod actually didn't exist anymore, the item would have failed to load from the database, and you couldn't apply currency to it (and we'd have recieved warnings and be looking into what happened to the item).

In the situation you're actually describing, that mod still exists in the game, but new unique items of that type no longer generate with that mod. However, that's only relevant to generating new unique items, which you aren't doing. Your item has that mod, so the Divine orb will re-roll that mod within it's current stat range. This can still be easily done because that mod is still in the game and thus has that range data.

It's very likely that the stat range for the mod hasn't changed, since there's little point in us changing the range on a mod we're no longer going to generate on new items. It's possible, however, that the range might have been changed, even to a range of (0-0), which would effectively "remove" the mod (the item would technically have the mod, but grant a value of 0 of it's stat, which is the same as not having the stat, and said stat wouldn't be described on the item. I'm not aware of any specific case where this has happened, but if, for example, we removed a drawback mod from a unique and wanted people to be able to "remove" it from existing items with a Divine orb, that would be a way to achieve that.

The league you're in doesn't (and I'm pretty sure can't) matter.