So essentially this article states that Trump and his team knew Flynn was under investigation for his work with Turkey / Flynn Intel Group, and NOT the Sergey Kislyak stuff, but they picked up the Kislyak stuff because they unmasked Flynn's name and started investigating.
This part here suggests that the Kislyak investigation was already underway by January 4, 2017, when Flynn told McGahn he was under FBI investigation for Flynn Intel Group.
As noted in Ali Watkins' article from March 15, 2017, the FBI was prepared to close the book on Flynn 'until the Logan Act stuff'.
The first mentions of the Kislyak / Flynn calls happened in an opinion piece titled "Why did Obama dawdle on Russia's hacking?", written by David Ignatius in The Washington Post on January 12, 2017.
washingtonpost.com/opinions/why-d…
washingtonpost.com/opinions/why-d…
During an interview on January 15, 2017 between Reince Priebus and George Stephanopoulos, Priebus said Trump had confidence in James Comey.
On January 18, 2017, Comey told everybody over a conference call that he was staying.
abcnews.go.com/Politics/week-…
nytimes.com/2017/01/24/us/…
On January 18, 2017, Comey told everybody over a conference call that he was staying.
abcnews.go.com/Politics/week-…
nytimes.com/2017/01/24/us/…
This tweet about Flynn having access to all the intelligence agency secrets is clearly why they had to get rid of Flynn first.
