This is what I did, it worked for me:
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Moved the files back to PC/MAC, they all came back to normal.
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Restored the NAS to initial condition (no data, no settings). There is such an option in ‘advanced’ (If I remember correctly).
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Moved the files back to NAS.
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Didn’t touch twonky, didn’t even enter it.
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Left all shared folders empty just in case.
Everything works so far.