Since you are a member of the Best Practices Course, I suggest you review the section of the course on library management, which will help you understand the options available here.
One option in ArchiCAD 14 is to highlight the problem LCF file in the Linked Libraries list, and click the button to Embed the library into your project. I believe this may automatically remove the duplicates during the process. If you later need these library components to be available for other projects, you can highlight that embedded folder in the list (after you finish embedding it) and then use the button to save a copy of the embedded library (hopefully, all cleaned up) to a disk folder.
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