It does seem strange timing considering he just interviewed the man who has clearly endorsed such a huge conspiracy theory..
Assuming what you say is true, any bad publicity tends to make people more curious and look into it which is probably what Flynn wants. Reverse psychology..
Imagine the reaction when those who thought Q was a bullshit conspiracy theory suddenly realise Q is very real and someone like Gen Flynn is probably one of the people running it.
It might take them a while to pick their jaws up off the floor but it would also be the most talked about 'thing' at that moment in time.. The world will definitely be watching..