Would anyone know if having all of the 'diverging paths' [...] in my savefile would break it?
I'm on my first playthrough, ever, and actively tried to not get a comprehensive view of how things work. So I'm not an expert, not at all. Some insights were unavoidable, though.
My expectation is that future edits will become necessary as you go along, but not all that many. If I'm wrong and you have opened an unmanageable can of worms, you're going to find out very quickly.
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ETA, my own question of the day: should I keep my Codex vessel (Fortuna)?
I've just had my first Space Freighter and was dismayed that it requires an interplanetary craft; I can't well keep both the Fortuna and the Drakkar at hand, and swapping vessels between outposts as needed is such a PITA. It seems as if the Fortuna has become mostly obsolete by now... or is there something I missed?