Brilliant, thank you, no idea how ULMF slipped my mind. Sadly there seems to be no fix, but plp report the same problem and there's a full save. Now I can confidently say I didn't waste my life completely last night.
As for the game itself I only know of the torrent on sukebei, which I'll make sure to seed:
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A note if you're going to try using Visual Novel Reader, make sure to turn it off before saving or interacting with any of the crystals - for me the game immediately crashes otherwise. Restarting it usually gives you enough time to save (which you should do often and in several files if you encounter problems like I did).
Edit: so I did some extra research, and I'll now strongly suggest you get translator++ and a rpg maker decryptor instead of VNR.
Translator++
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Decryptor
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And a handy video guide:
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I'd personally also recc using a save editor and boost the hero because like any RPGMaker game the combat is a grindy sludgefest of giant rats and bats.
But at this point I'm probably preaching to the choir.