This should initially be resolved by calling out the difference in handling in the docs. In short when you use vdb imports in embedded the import is processed at deployment time only. If the imported vdb later changes, it will not cause any changes in importing vdbs.

Note that in teiid-syndesis this import management logic was added via a custom vdb lifecycle listener, but that isn't quite the best solution given that we shouldn't be doing a lot of work in that thread.