Looks like you are on the right track with the persist-flush-refresh sequence. Yep, I
think em.persist() would be more suitable.
If User is the owner I doubt you want CascadeType.ALL on the Group's Set (which you
have as Set which I suspect is a typo?). Perhaps a subset of ALL?
Regarding updates, you can just update an entity, and, assuming cascade is on, it will be
merged to the database at the next flush (explicit or implicit at transaction boundary).
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