Two things are clear: (1) Flynn’s interactions with Russians were not illegal; and (2) he never should have talked with Mueller. Trump should pardon him.
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Time for pardons comes a little later.
Item #1 is correct. Item #2 isn't relevant. Flynn's problem didn't stem from anything he said to Mueller's team. It dates back to when the FBI interviewed him in December 2016 or January 2017. As Trump's nominee to a senior national security post (National Security Advisor) he would be subject to a background check and couldn't refuse to meet with them.