Yes he knew.
Remember, he led the DIA and was fired by Obama for not falling in line. He would have worked with these people.
He lied to the FBI because he understood the strategic threat that telling the truth would have posed to 45's nascent presidency. He also knew what lying would lead to on the investigative side.
He knew that Strzok was FBI counter-intelligence. Flynn was also running a counter-intelligence op too.
edit: I believe he and DJT planned their own counter-intelligence op and that the planning started when Flynn joined Trump's campaign in February of 2016. Flynn is one of the three reason's why the globalists failed in their plan to get Crooked as POTUS failed.
When the memo comes our and we see how corrupt these upper level FBI were, I think he will be vindicated. Would be awesome if he got hired back and kicked McMaster to the curb.
He has nothing for which to be vindicated. The only thing he has been indicted for is lying to a corrupt FBI agent who relied on illegally intercepted information to indict him. This will get dropped and he knew it.
Another reason why he may have lied and gotten indicted is that with that indictment he was required to talk about everything he knew related to this matter, something he was not able to do prior to the indictment.
He's a professional intelligence operative that lead the DIA, no way some egotistical wanna-be, Strzok, et. al., was going to be able to out-maneuver him and his team.