What is happening seems to be this:
Let's say we have an @Indexed entity called Son. It has @IndexedEmbedded parent property called Dad in @ManyToOne relationship. Dad is @ContainedIn and has @Field on one of its fields. I am demonstrating a condition when more than one Dads are updated in a single session, only one would be re-indexed, the rest will fail to be re-indexed.
I am attaching a simple IDEA project that clearly demonstrates what is going on. I believe that this is a very serious bug. (Note: I removed hibernate-3.6.0.jar from the lib directory to minimize the size of the zip file under 10M, the rest of the jars are there).
Please run BugDemonstrationTest#showBug test method to see everything.