Not exactly sure how it works, but what you're doing could get you banned by Nintendo. Apparently they frown on out of region titles. The eShop can't find your update because it doesn't "have" it. You can't update out of region games. You're just going to have to go download the updates from that iso/chaos site.
When you say blank screen, do you mean the Nintendo 3DS logo black screen or is it really a black screen with nothing on it? If it's the screen with 3DS logo, it usually means you're missing the seed. Go in FBI, go to Titles, find the game, and Import seed.