I have taken my ship to Menelaus and back to overworld, and back to Menelaus, and then I tried to lower it on Menelaus. I had plenty of Neon Energy but the percentage did not complete and the ship did not move.
I could no longer get back to overworld, so I broke the BoardComputer and made another one.
That one would not move the sihp, so I made another one, and my son placed it and we went back to overworld, but and I am not sure which part of those attempts messed it up, but the ship made it back to overworld at the correct (same) X and Z but it was now high in the sky. A few attempts to lower the ship (x=0, z=0, y=-70) did nothing. A few attempts to move the ship (x=10, z=10, y=-10) did nothing. The percentages are all over the map. It can get stuck at 42% or 99% or it can indicate 320% or 156%; (those number are approximates. I did not write them all down.
I made another BoardComputer and went back to Menelaus and back to overworld... still high in the sky.

The high is saved in the BoardComputer so when you break it, the "start high" from the overworld will be lost. I nead to look into why the percentage doesnt complete...

I considered the Neon Energy problems but when I used the Scanner I didn't have the same good details like the Researcher (sneon: some number, neon:somenumber).
I had it next to a generator with a bucket o lava, and on the otherside a battery block that i started with Neon Batterys that I found, and then crystal batteries that I gave my self using creative mode (just to see if it would help).
Thank you for investigating.