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I have not looked at the code in detail but my guess is that the migration step is run before the Model synchronization (that is when there is dynamically created proxy classes are created that "links" together the typed properties on your model class with the backing PropertyDataCollection).
If that is the case then you could try to access the data the "old" way as:
(model.Property["ContentReferenceToBeCopied"] as PropertyContentReference).ContentLink