Don't know where you read that.
The common standard is to have three libraries for each project. The standard ArchiCAD library, an office library with parts that the office has made or had modified to suit, and a project library (this could now be the internal library) with parts specific to the particular project.
None of these should have duplicate parts (that would result in error messages). If you are finding duplicates, you would want to first removed the part from the internal library (this is the most fluid), then the office library (take more care here), then the ArchiCAD library (But just don't do it).
Erich
AC 19 6006 & AC 20
Mac OS 10.11.5
15" Retina MacBook Pro 2.6
27" iMac Retina 5K