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If you create a model with two related classes A and B, and one navigable relationship from A to B. You will lose the relationship if you generate the code and next try to do reverse engineering re-creating the original UML model.
During Reverse Engineering new elements A and B and an aggregation (as there isn't enough info in the java code to distinguish what does an attribute represent - an association or an aggregation - an aggregation is created) was deduced from the source code. They replaced the old elements. The old association between the old elements was deleted. A merge logic must be added into RE to try to identify and match between relationships already existing in the model and ones that are produced by source analysis during RE.