Alright, so after going to the coordinates that Shanice extracted from my bot and going there, after a few days my character automatically goes for a walk to think about how he should proceed. When I come back Jun is missing and I keep going through this loop of trying to fix this. I even tried making her like me so much to the point where I get the bed cuddling event. To my surprise even that didn't work. So I'm on my wit's end trying to figure out what went wrong. Anyone got any insight on what is happening?

That's because you lied to the priestbot. 

Spoiler: If you lie to priestbot he doesn't go with you to research the coordinates If you don't he does finds a camera and disables it. Find an autosave before you lied to him!