Don't worry, your 3D map is probably still there. I'm hoping it's still there.
Due to the nature of PCG, Josh's youtube videos only showed a snapshot of what he was working on at that time.
He has said previously that the code is still there, he just does not show it in other videos as it was not pertinent to the video being shown for that month.
You will see in Update #12 he goes into how he is able to drill down from the System Star Map, using the Nodal UI, to individual objects https://www.youtube.com/watch?v=ADcfqusFfaM&t=8m49s
(He shows and talks about this between 8 mins 49 seconds and 9 mins 30 seconds.)
PCG is modular, and Josh is able to turn on/off different functions (Nodal UI) as required.
Here is the link to the Nodal UI in Update #11 (your link points to Update #21)https://www.youtube.com/watch?v=Ekq56VZqQvs&t=4m53s