We are aware of issues with legacy exon numbering, as we have handled similar issues with variants (such as IVS nomenclature with legacy intron numbering). For now, CNVs are normalized by matching the exon numbers to the longest transcript and mapping that to the GRCh38 reference build.
You can easily see legacy citations using different exon numbers by searching for deletions or amplifications of the entire gene, then sorting the CNV list based on start position to see references using alternate exon numbers. You could then click the legacy exon numbers and sort the article list by publication date to focus on older articles more likely using legacy numbering.
If you are aware of specific genes and examples of this issue, please reach out to support@genomenon.com and let us know so that we can consider incorporating corrections for the genes into our Genomic Language Processing pipeline.