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We've experienced several issues maintaining alternate over the last year that have resulted in bug fixes. Some of the issues were related to using the function HierarchyDeleteAllElements. As a test, I would suggest deleting and recreating the hierarchies using HierarchyDestroy and HierarchyCreate and see if that resolves the issue.
Here's a snippet of an email I had with one of the developers that may provide some insight…
TI follows the metadata edit pattern of duplicate, modify the duplicate, dimension update. But it does the duplication and update automatically, duplicating during Prolog/Metadata when calls like HierarchyInsertElement occur, and updating at the transition from Metadata to Data tabs.
But the Dimension/HierarchyDeleteAllElements TI function uses an old trick. They don't take the duplicate. Instead, they introduce an "duplicate" that is just a brand new, empty, unregistered object. The code that auto updates at the Metadata/Data transition doesn't know the difference.
If delete/recreate resolves the issue I would suggest submitting a support ticket.