Unfortunately it seems like when the chunk for the hyperbox is loaded, all lighting turns into a 1 block wide spot, and it doesnt illuminate the whole area...

https://imgur.com/a/BRWmroW

This ends up preventing any crops being placed.

This doesnt seem to be an issue when the chunk is not loaded.

Using ftb chunks to keep both the outside and inside chunkloaded
So far it fixed when I broke the hyperbox and placed it again, will go to keeping the parent chunk loaded only

does this work if there are hyperboxes inside of hyperboxes?

When you have hyperboxes inside of hyperboxes, as long as the parent chunk is loaded, the outer hyperbox will be loaded, and therefore so will the inner hyperbox (or at least that's the intention)

Actually, I just checked, I have another hyperbox chunkloaded and the lighting isnt breaking there, the only difference between them is that broken lights box has pipes leading to the apertures.

Just checked and nope, the lighting still breaks anyways even without the aperture being used

Are you using something to keep the chunk from unloading?

Are you keeping the internal hyperbox chunk loaded, or the parent chunk in the outer world unloaded?

Hyperbox already keeps the internal chunk force-loaded while the parent chunk is loaded, so if you forceload the internal chunk yourself then it might cause strangeness. If this is what you're doing, does it work correctly if you keep the parent chunk loaded instead?