Did you even read the article you linked?
Flynn isn't even the one accused in that case and the charges that were dismissed were in relation to failing to register as a lobbyist for a foreign government. If it was a totally bogus case it wouldn't have gone to trial.
Flynn's cooperation with Mueller is what led to the indictment of this guy, Flynn was his business partner.
As mentionned in the article:
Kian and Flynn worked together prior to Flynn joining the administration as part of the now-dissolved Flynn Intel Group, NBC News reported.
Their work, which included efforts to see an elderly Muslim cleric extradited from the United States to face charges in Turkey, was not properly disclosed to the Justice Department.
And the conviction was tossed which says there was nothing there.