For the Keycloak project, I was able to reproduce the following:

• Run Hibernate 6.2.0.CR3 on Quarkus aka Bytecode enhanced
• Load an entry with a collection (ElementCollection in our case)
• Replace the collection with a new collection
• Run an unrelated query to trigger an autoflush test -> this will initialize a CollectionEntry with ignore=true, so it will be ignored throughout this session
• commit

Expected result: Only new entries are in the database
Actual Result: Old and new entries are now in the database, als the old entries haven't been deleted.

This problem doesn’t occur when bytecode enhancement is not used.

Reproducer test case: https://github.com/ahus1/hibernate-test-case-templates/tree/is-HHH-xxxx-element-collection-after-skipped-autoflush