It still reported the error likely because you started the shard then closed it without saving, meaning the new file existed but had no data in it.
Because the file didn't have to be created again, it warns you that it's an empty file.

Save your world before you shut down, after the first save with the new Persistence system is done, you won't see the error again unless your data is corrupt.
 
He has the updated version, the fix I added was to catch the EndOfStreamException and display it rather than allow it to totally crash the shard :)
 
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