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Are you using two different libraries? Cleaning the books up in one library then copying the books to the other library? Your work flow talks about folders not libraries, so I'm a little confused.
I set my automerge to create a new record if a duplicate format is found. Then now and again I run the find duplicates plugin and if 2 library entries exist for a given book I analyze which record/book I actually wanted in the library and delete the other.
Thankfully this rarely happens in my workflow but when it does I don't lose anything.
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