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Can we confirm the steps followed here?
1. Seamless data pump loads data from SCCM into a staging dataset in CMDB
2. You normalise the staging dataset with the above Product Catalog Alias Mapping in place (i.e. you run a NORMALIZATION job, not e recon. job)
3. After normalisation, the product CIs don't have the required product cats. It still has the original SCCM values set up for you by the Seamless Data Pump.
Do you also have normalisation rules defined (i.e. via the NE alias form??)