I'm getting that vanishing items thing now - Seperate from the previous one, removing them manually this time rather than stripping the entire ship (Although in retrospect maybe the same thing is happening?) - and it turns out that the items aren't actually being deleted? Just... Not actually removed?
Only tried this with cores since I didn't have a colony item set to the ships, but I removed the core, Alphas, checked inventories, nothing. Put in another core, Beta this time since I was out of Alphas, checked inventories, and the old alpha core showed up in my inventory. Tried it again on another ship that I'd pulled the Alpha from earlier, put on a Beta, and the old Alpha popped up in my inventory.
I was actually checking something else. My first thought was that maybe it just didn't work right when refitting on owned planets? So yeah. I'd pulled the cores on my planet, thought I'd lost it, and grabbed stuff to try at a npc planet instead.
Edit - Same issue pops up on Epta.
2 - Yeah, same thing with colony items. I'm cycling between a couple items here, pulling a item won't return it, but if you have a spare of the same item then you can reinstall it and the item won't be taken from your inventory. Or maybe it's pulling the new item from your inventory and finally 'removing' the old one from the ship. idk which.