I'm having the same issue. I didn't notice the problem until today. I spent the last hours figuring out why my data is not syncing until I found this post. I'm using the same approach, restoring Core Data from a big JSON file with a lot of many-to-many relationships. At least now I know that the problem is not on my side...
Topic:
App & System Services
SubTopic:
iCloud & Data
Tags: