thats somewhat difficult to point at something specific in your process, because there are so many potential places where the bug could hide ;-) providing some pseudo-code could also be helpfull.
however: to be more specific, it seems that hibernate looses the state of the parent-children-relationship, so the problem seems to reside in your synchronization of the original Set of your Parent-Object.
please check, if you somewhere dereference the original set. For example, just setting the parents set to your new children set or the like.
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