Hello,
JPA queries will refresh referenced objects if you have the cascade refresh options selected. Otherwise, just the initial object itself will be refreshed (which includes rebuilding references, and so lazily relations will be reset).
I don't know the reasoning behind it not being on by default, but I believe it will be configurable within EclipseLink without having to use customizers. You may want to file a request to get it turned on by default in TopLink Esssentals (and preferably in EclipseLink).
Best Regards,
Chris
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