The main problem is that entity keys are not removed from BatchFetchQueue#batchLoadableEntityKeys when entities queried in the batch are not found. As a result, the same entities will likely be included in future batches (as reported above).

I've create a pull request [1] that contains a test case (BatchFetchNotFoundIgnoreDefaultStyleTest#testMostNotFoundFromQuery) with comments thatt spell out what is happening. In this test case, an entity class has an optional one-to-one association that is annotated with @NotFound(action = NotFoundAction.IGNORE).

There are 8 entities persisted with a non-null one-to-one association. The associations for the first 7 are deleted. When the entities are queried ("from Employee e order by e.id"), we expect the associated entities for the first 7 to not be found; only the association for the 7th entity will be found.

As the query results are processed, the entities keys for entities with the following IDs are added to BatchFetchQueue#batchLoadableEntityKeys: [0,1,2,3,4,5,6,7]

Batch query:
select batchfetch0_.id as id1_1_0_
from Task batchfetch0_
where batchfetch0_.id in (?, ?, ?, ?, ?)

When processing associated entity with id == 0:

• batch query is executed with IDs bound to query: [0,1,2,3,4};
• none of the entities are found;
• associated entity with id == 0 is set to null.

BatchFetchQueue#batchLoadableEntityKeys still contains EntityKey for entities with IDs [0,1,2,3,4,5,6,7].

When processing associated entity with id == 1:

• batch query is executed with IDs bound to query: [1,5,2,3,4];
• none of the entities are found;
• associated entity with id == 1 is set to null.

BatchFetchQueue#batchLoadableEntityKeys still contains EntityKey for entities with IDs [0,1,2,3,4,5,6,7].

When processing associated entity with id == 2:

• batch query is executed with IDs bound to query: [2,5,6,3,4};
• none of the entities are found;
• associated entity with id == 2 is set to null.

BatchFetchQueue#batchLoadableEntityKeys still contains EntityKey for entities with IDs [0,1,2,3,4,5,6,7].

When processing associated entity with id == 3:

• batch query is executed with IDs bound to query: [3,5,6,7,4];
• associated entity with id == 7 was found, put in the PersistenceContext; none of the others are found;
• associated entity with id == 3 is set to null.

BatchFetchQueue#batchLoadableEntityKeys still contains EntityKey for entities with IDs [0,1,2,3,4,5,6]. The EntityKey for id == 7 was removed from {BatchFetchQueue#batchLoadableEntityKeys}} when that entity was added to the PersistenceContext.

When processing associated entity with id == 4:

• batch query is executed with IDs bound to query: [4,5,6,2,3];
• none of the entities are found;
• associated entity with id == 4 is set to null.

BatchFetchQueue#batchLoadableEntityKeys still contains EntityKey for entities with IDs [0,1,2,3,4,5,6].

When processing associated entity with id == 5:

• batch query is executed with IDs bound to query: [5,4,6,2,3];
• none of the entities are found;
• associated entity with id == 5 is set to null.

BatchFetchQueue#batchLoadableEntityKeys still contains EntityKey for entities with IDs [0,1,2,3,4,5,6].

When processing associated entity with id == 6:

• batch query is executed with IDs bound to query: [6,4,5,2,3];
• none of the entities are found;
• associated entity with id == 6 is set to null.

BatchFetchQueue#batchLoadableEntityKeys still contains EntityKey for entities with IDs [0,1,2,3,4,5,6].

When processing associated entity with id == 7:

• the associated entity with id == 7 is found in the PersistenceContext, so no extra query executed.

BatchFetchQueue#batchLoadableEntityKeys still contains EntityKey for entities with IDs [0,1,2,3,4,5,6], and will continue to contain these until the session is flushed. If any other Task entities are loaded before flushing, the batch queries will continue to include 5 parameters.

[1] https://github.com/hibernate/hibernate-orm/pull/2014