Well I didnt have enough plots on my main, so i put a beacon in the middle (not that whole area btw, it was only in the middle). Anyway I used 4 plots, at a height of 3, totalling 12 plots total. When I had enough plots on my main, I simply removed full vertical plots of 3 at a time and plotted them with my main until eventually I ended up with the beacon that belonged to my alt which I removed, switched and took them with my main.
The area I showed in the picture is much larger and more irregular than that, so I doubt that was the reason as this shows an L shape of the area that originally belonged to my main in the first place. Also, the underground road and room network was also my main and was never touched by my alt and they are gone too.