The judge can judge st through w the case out with prejudice.
I would guess that if Manafort wins on his challenge to the Special Counsel authority, the case is dismissed without prejudice.
The local US Attorney could go back to the grand jury and get an identical indictment from them and start the case again under the authority of the local US Attorney.
I saw one of search warrants. It was sworn out by an FBI agent, not by one of Mueller’s sleazy lawyers.
If all of the search warrants were handled the same way, the local US Attorney might still be able to use the evidence seized in a new re-filed case.
But if the case has to be given to the local US Attorney, he may have more important cases on his plate and might not pursue it with the same lunacy as Mueller.