I'm not really sure about this but I think it's the saves log (or smthg like that, I don't know how to call it exactly haha). I mean, did you delete the first version you've been playing then downloaded the updated zip version?
actually, wait, do you use desktop or cp? >>
I also think that if the saves log is the problem, with it all gone, I'm afraid it can't be retrieved.
I'm only speaking base on my theory and small knowledge about exported game files, so I don't know if this will really be of help.
the folder for saves should contain smthg like this, if it's empty then yey everything is screwed '-' hope that you'll soon retrieve the files if it was only a bug :))
[to see the folder I attached as an image just right-click the andromeda six shortcut then tap locate game files after that go through the games folder and you'll see the saves folder (ofc click it to see the content lolll).]