I might have to work around the deletion limitation case by either treating deletes as updates in the eyes of Hibernate Search with a status field and simply eliminate the deletions via application rules applied on the queries but I would expect that might not be so efficient.

Hibernate Search already does something similar: it removes from resultset elements which are not matching a valid entry in the database. That's what I was referring to when I said above "deletions don't affect the actual results but could slow down the queries by bloating the index": and you're right it is not ideal from a performance point of view, but at least it doesn't impact correctness of functionality.

On the rebuild in another Directory: yes we discussed similar approaches and I'm inclined to agree that it might be the more effective solution. The downside is that it would require specific support in multiple subsystems and will break user extension points like custom IndexManager or DirectoryProvider_ implementations. I'll need to explore some to see the impact but indeed it's hard to think of a better strategy