The docking in the video is as clean as I can get really. It may look weird because I came at it from an angle but that was basically straight up into the bay. Even the Seamoth clunks as it enters.
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That's a pain to do every time you want to change a simple thing if you have a lot of panels. Slightly less painful is to just make your changes then use "nocost" to rebuild them before turning it off afterwards.
I can confirm this problem too on build 31112 Apr-2016. From what I can see the OP has nailed it pretty well. Any time you modify a building, or a building attached to the one your solar panels are on, the game deletes the solar panels. It's particu…