Hello, I post a new thread since I'm not sure the bug is related to the other ones here.
I was surprised to see that I was not receiving the ressources I asked to craft some chip for armor (night vision, etc). and was surprised to discover I was back at the vanilla number of slot.
I try your command but it disallow achievement so I can't really use it.
I was thinking about perhaps the chip you can made in nanobot was culprite so I go in creative and just set a train to die, in order to actually reset and recover my slot. After a few test, you don't need any ship to run into this bug. As soon as I wear an armor, I lost my slot. Removing it doesn't give my slot back. Tested with the light armor, the modular armor and the MK2 armor.
I don't have any mod, part this one, that actually add or remove logistic slot.