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I have a site which has some content types which have custom entities which refer to them.

The exact example we are using is https://drupal.org/project/registration. We have event nodes which have registrations. I need to export all the nodes and the entities which reference them. The Node Export module works fine for nodes but misses these entities. And of course, besides for actually exporting them, we need to maintain the node/registration relationship.

What is the best way of doing this?

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My solution for this was to use the Migrate module. It is very powerful and you can create update classes for custom entities when one doesn't exist from the producer of the contrib module. I would highly recommend it.

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