you don't give enough information. But hibernate does not destroy relationships :-)
I have a user with id 1 and name "A" and a group with id 24 and name "B".
They're in a relationship with an entry in the Join-table.
Then i update "A" by doing
User u = new User(); u.setId(1); u.setName("Z"); manager.merge(u);
and after that the entry in the join-table is gone. I can change the group like this without destroying the relationship, though.
fundamental mistake on my side? :)
Still could use a little help