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I am using Windchill PDMLink Release 12.0 and Datecode with CPS 12.0.0.0
User facing one issue like, Windchill not reflecting where used report for alternate components/parts.
This is correct but working to spec. If you want to include alternate or substitute parts in a where used report, you will likely have to create your own. The stock report only navigates WTPartUsageLinks. There are other links that handle replacements.