And he did take money from Putin and lied about it. There may be more than we know, but the story below is something you seem to forget.
You don't stop being an asset when you get promoted. In fact, you become an extremely valuable asset. Which is why the DAG went to warn the White House about him.
He was a paid agent for Turkish interests. Note there is a difference between "agent" and "asset." It's important. And there is no way for us to know (yet) how much he did for Turkey, or when, or when he stopped. But because he lied about the payments, the Turks had leverage over him, too.
REMINDER: This is all just what we know. Mueller and the judge know a lot more.
Sorry if these are inconvenient facts.
Link: https://www.nbcnews.com/news/us-news/flynn-lied-investigators-about-russia-trip-says-top-house-dem-n763216