Almost all modern Bibles, including many King James Bibles, change the word “throughly” to “thoroughly” because, they say, it means the same thing. Throughly is just another archaic word that is no longer used, so they change it to thoroughly.
But ‘thoroughly’ is also used in the King James Bible, so it is apparent that they deliberately chose to use throughly when they did.
Although the words are similar, they are not the same. Throughly has a meaning that is different and distinct from thoroughly.