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Locating orbital POI.
I don't even bother trying to explore in space anymore, there is no reliable way to know where you have covered and where...
I have noticed this as well and I think it might even be an "auto landing/docking" feature. When hovering over a base it gently lowers the vessel...
If your HV is close to the surface, you might be able to relocate or add extra hover engines above the water.