The charges against him in the Washington case include conspiring to launder money, conspiring to defraud the United States and failing to register as a foreign agent. In Virginia, he faces charges that include bank fraud and filing false tax returns.
He has pleaded not guilty to all of the charges, none of which are directly related to work he performed for Trump's campaign.
In both criminal cases, Manafort has asked the courts to dismiss the charges on the grounds that Rosenstein's May 17, 2017 appointment order hiring Mueller runs afoul of Justice Department rules on special counsels.
Ellis is not obligated to follow the Berman ruling, but it's unlikely he'd reach a different conclusion. Even if he did, the case would just be handed over to the local US Attorney, as the Cohen case was in NY.