Good point.

The solution would be to have a separate instance of org.hibernate.search.engine.spi.DocumentBuilderContainedEntity for each root point. For example if "Author" is embedded in both entities A and B, you'd have a different builder instance for A.author and B.author; at this point each instance of DocumentBuilderContainedEntity could be flagged as "belongs to indexmanager X" and hold the information you need.