Well I have theory, as many people here is keen to know how many people knows Conan's secret. Heiji knows as he's persistent. And recently everything is done in the dark, I've read the manga and every characters lurking around, see you here and there... I can confirm with everyone there's inside story.
Megure is important figure, as no one haven't recently notice him. The only happening is they have Conan's cellphone. Why Megure is important? He will think Conan is illegal immigrant when he noticed Shinichi's fingerprint on Conan's cellphone, he's not going to like it but it's likely he don't want to believe. He will ask Takagi and Satou about the kid. He likely to think Conan is related to FBI and receive their protection if this goes on (he's going to have third thought). And Megure won't let this rest, I think in dark he wants FBI to investigate as terror has taken place before, in shopping centres and areas which has been bombed before. one thing I'm a bit uncertain, he maybe incline to think the terror act does relate to FBI.
I think... it's matter of time Megure will find out Conan's cellphone, if they collaborated to accept Akai want to fake his death. And Takagi somehow able to give new cellphone straightaway, as Conan may tell Takagi in advance about incoming event of Akai's major decision. Takagi is frank, so he has decision to help Conan either to keep secret or seek for 'army'.
When Akai is alive in hospital, they don't know Conan's secret, but story so far proceed to Takagi's suspicious act and behavior around Conan. (that's what we gather when reading manga) Megure act or innocently show he doesn't know, but I'm clear about he's still investigating 'Conan and Haibara's kidnapping case', for one thing I'm certain he know that case meet more than an eye.
So I can gather, Megure see Conan is a mysterious person he ever met in his life. He knows Conan received help, has unusual name, still planning to find out more about 'kidnapper'. Maybe he knows of Conan's cellphone is in the police force, realize there's no Conan's finger print as he realized they don't have 'child's' finger print. the deleted scene, or hidden story... Megure will not going to ask Conan about it. He will ask Shinichi's parents about their son and the alias 'Conan Edogowa'.
Based on this evidence he has, he will search for what opponent he's up against that has caught FBI and Shinichi's family in fear. (We may discuss more of plot in this thread, as there's Sera involve deeply.) I type this up so I can think better, the manga will continue tell the story about B.O. soon.