Just in case it still matters…
I sorted this problem in this way:
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Opened my existing library, selected only those refs I need
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On right click chose “Copy References To”, then “New library”.
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Closed all libraries.
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Physically deleted file of the original library (with all crap I do not need in it).
5. Sighed with a relief.
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Opened the new library and saved it as my original library name.
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Deleted the new library file.
Hope this helps.