Why is Chiisaku Natta Meitantei considered the "real" first episode?
That is a two-hour remake of the original 1st episode, in celebration of the anime celebrating 20 years in broadcast. The special retells what happened on the day Shinichi’s was transformed into the body of a child. The special includes new scenes that weren't in the original manga or the first anime episode. 

https://www.youtube.com/watch?v=T_g9zHvMXBQ