Post-NEXT the 4 in my freighter reappeared, though in a different order, then disappeared, reappeared, vanished again. Stuff this, I thought yesterday and bought a c class hauler that landed aboard. And filled it with stuff.
Now it’s gone too!
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It’s intended for your ships to not spawn in when you call the freighter somewhere but saving and loading that save on your freighter will make your ships appear again so all is fine. You don’t NEED to go to your freighter to change ship anymore…you can now just call any ship in your collection to you pretty much anywhere and swap on the go.
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Its intended? See I don’t like that because then it begs the question where do your ships go? I prefer to have my ships on my freighter I want to see them nice and displayed plus easy access to switch them. I’m old-school I’m never going to summon my ship on to a planet. 
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Well they patched an issue where the ships wouldn’t show up for people when loading a save made on the freighter…so presumably they intend things to be this way…though I agree it’s far from an elegant solution. As for where they go…who knows…they go hang in the void between simulations! 
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K, thanks for clearing that up. The freighter subcontracts to myHermes.
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