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Can you post your exact author sort plugboard command.
Do you get any warning or dialog windows that states that one name will overwrite another?
It sounds similar to an issue I saw where the plugin would find one collection with certain books in it, and then later find that same collection name due to the splitting/translating and overwrite the books in the first collection. I added a check for this to warn.
I'll try to reproduce this but may need to post a debug version for it.
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