They went after Flynn not because of this but because Flynn was trying to head off Obama and John Kerry’s moves against Israel at the UN in December 2016. They and Russia were pushing a divestment movement against Israel for settlements. That’s why Kerry was zipping all around the world at that time trying to organize other nation’s votes, and why he pulled that weird last minute trip to the Arctic....as an excuse to get to New Zealand to secure their vote. Flynn was countering Kerry’s moves.
However….ahem
Flynn’s son was becoming VERY vocal on social media about pizzagate, Comet PingPong pizza, etc
I believe part of the deal Flynn accepted was to save his son