Yes we have the same issue. I think the API returns the username for an inactive account in a slightly different form which is what causes the discrepancy.
As a workaround we have added a custom personnelAlias aliasPool value called SAILPOINT_ID to our Cerner accounts.
Then we are using a customization rule to parse that value out of the personnelAlias and populate a custom field I added to the Cerner Schema in Sailpoint. (This allows for easier Correlation)
We haven't been able to get all of our Cerner accounts populated with the new personnelAlias value. but I am populating that value as I touch and provision Accounts. so moving forward we should be able to correlate more and more of the Inactive accounts.
We also experienced that same issue. We created an attribute on the Identity for the cernerId and updated our correlation rule to use either username or cernerId. As long as the Identity exists, it seems to be aggregating and joining correctly.