The thing very few have realized about the Logan Act that many are realizing today is that *secretly negotiating with a foreign power* is basically the *definition* of "collusion."

So whether a Logan Act probe was ongoing or not, what Flynn did was violate the act—and *collude*.
PS/ The investigation ongoing into Flynn in late 2016 was a counterintelligence investigation; a criminal investigation came later. But the *concepts* undergirding the Logan Act, a criminal statute, are actually even more *richly* in play in a *counterintelligence* investigation.
PS2/ The question being asked about Flynn in late 2016 was not if he was a Russian agent—but whether a foreign power had such leverage against him (e.g. nonpublic info) he'd be considered compromised and a national security threat. Secret negotiations with a US foe? That'd do it.
PS3/ One way of explaining how different being an *agent* is, is to consider Papadopoulos. In that case, the Russian Ministry of Foreign Affairs wanted a specific task completed—a Trump-Putin backchannel—and used an intermediary to secure Papadopoulos's services in completing it.
PS4/ Papadopoulos's informal but agent-like agreement to execute a Kremlin-set task was nonpublic info he wouldn't have wanted out, but not criminal per se—so the compromise was fairly weak. Flynn, while not an agent, committed a crime, thus giving better leverage to the Kremlin.
PS5/ Beyond not realizing it's a *legal* as well as CI concept, many think of agent behavior as a binary in which one is nothing or a slave. In fact, Russian intel operations typically start with a request being made of the target to complete a small and likely non-criminal task.
PS6/ Here we might use Trump national security adviser Carter Page as an example. When Russian intelligence wanted to develop Carter Page as an agent, it first simply asked him to deliver information about the U.S. energy industry. It was a test to see if he would execute a task.
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