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If you work with Creo Elements Direct Modeling, Windchill and Illustrate, the full scope of Illustrate cannot be used.
An Elements Direct Modeling assembly is opened and processed via Windchill in Creo Illustrate. If the structure in Elements Direct is changed afterwards, e.g. during an index change, Illustrate does not recognize the new structure. It will only tell you that there is a change in the structure and that parts have lost the connection.
For this reason, Creo Illustrate should be improved so that a structural change is not only recognized but also correctly mapped.
Illustrate uses the part ID + structure path to identify parts, this allows us to cope with multiple instances.
So the sort of restructuring you have shown will result in parts with missing links as they now have new path IDs.
It is recommended to keep any restructuring to a minimum in the eBOM as it will cause broken links in an update case.
Although these broken links can be manually fixed by the user, there is no way for illustrate to recognise a part has moved in the eBOM structure as it could be a different instance of the part.