Balder- no editor is going to accept EBCD as an entry. You have no choice but to come up with another 4 letter word or change the E to an A. You say you can't do this... Sorry, there's no alternatives. If you're not prepared to redo a section of the puzzle, large as that area may be, the puzzle would probably be unpublishable.
It is quite common for constructors to have to do extensive rework. Don't sweat it.