Can you please tell me which version you have played and (waht is actually more important) can you please attach your savegame file ?
This sounds like a game breaking bug and to find and fix is very important.
It's version 0.75.5 I believe this is the right save. If it is, you should be Maya's base.
If i spread the placeable areas too far on the island then the girls will not be located in one area anymore and therefore there are harder to find if the player wants seomthing from the girls.
This is why i would rather just declare a space outsite of the base as a placeable area for the machines (or.. make a quest out of it to make Marc build some ground to place them on)
If you just want to work with what's already there, the landing pad would be the best bet. It's already used for one event, so it could just be a big open area going forward. To accommodate this, there could be a mission to set up an alternate landing site for the supply shuttle.
For expanding the current base, I figure Yukari could say that the scope of the project has expanded, and additional space is required. The game would then load in a different map with an expanded base, if that's possible. The current base could also look a bit more lived in, with more of Malia and Maya's stuff scattered around.
As for an alternate offsite base, Juna's house would also be a good one, since she has such a large yard. As for the girls wandering around, you could put in a command that restricts their traveling, or have some version of the capture robot from AATOFL that you could command with your remote.
If you have read the lastest post on my patreon page then you know that this is exactly what i am working on right now (okay.. next weekend actually xD but you get the idea)
Sounds good.
This is a reallygood idea actually , but i would rather have it so that the girls would give clues overtime and they are getting more and more specific BUT you may loose the ability to tie them up if you take too long.. mhnn...
I should think about this more... (written down as an idea in my little textfile for ideas xD)
What made me think of it was the capture robot from your other game, along with the drone flying sequence from this game. Could call it Herding Cattle.
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One other thing that came to mind was using Milk as another form of currency. I figure Yukari could use it to trade information with other members of CORE. This could lead to new outfits, blueprints, and upgrades. I figure it could be a way to justify adding in stuff that wouldn't make sense within the scope of the base's research, like the flesh suits from the other game, or some special plants for the garden.