PCR duplicates are a result of a DNA fragment that was used to prepare the library has been sequenced multiple times.
CNVs are changes in the actual number of copies of a section of DNA in the cells being sequenced.
These are fundamentally different concepts. CNVs are identifed based on the aggregate coverage (and/or variant allele fraction) of the genome. PCR duplicate just affect one DNA fragment in the library. CNVs reflect underlying biology. PCR duplicates are technical artefacts of sequencing library preparations that use PCR amplification.