How can I destroy an empire-level title?

Solution 1:

Taking away all county level holdings of the current owner will not work, since he will just claim some from his vassals. You need to take over Every Single Territory owned by him, without taking the title. Once the title does not have any counties under it, directly OR indirectly, it should be destroyed and will allow you to create the latin empire.

Here is one source describing this http://www.reddit.com/r/CrusaderKings/comments/1azgns/how_to_destroy_the_byzantine_empire/

Unfortunately, this does require a series of wars against what is probably the most powerful empire in the game.

It's also possible to do this using the console commands listed here: http://ckiiwiki.com/Console_commands