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Use a Work Bench Library to do all of your metadata updates, and embed the metadata just before copying (with delete) to your "clean" Library. Use your "clean" Library to copy to the web. So, all of your Work Bench books, and none of your "clean" books, need embedding.
If a "clean" book needs to be changed, either move it back to the WB Library before doing so, or immediately embed its newly-changed metadata.
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