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add message if one of referenced entities is missed, may be add toto section to one of available entities. see issue #173160
it's good to add verification if not generated entity class[es] already exist and try to add relationship if classes are not read only, but as it's just one of case and may require some complex handling or may not work well for bidirectional relatonships if added to one class only when second one is in library and can't be modified it's not a part of this issue.
It's possible now to select existent entity for update/recreate, and new members should be added in this case. Still may be good to add a relationship even for unselected entities, but it's less important now.
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss