Lost user data with app update using CoreData + iCloud

I recently added iCloud support following Apple's programming guide and was able to release an update that successfully migrated the existing store to iCloud - enabled CoreData, and for a few weeks everything in this update did a great job dealing with user complaints.

Since then, I've started very minor code change code that doesn't even touch the CoreData stack, and since then, users updating the app experience their CoreData completely wiped out by the update. I have been going through the programming guides and posts for many days now, but I cannot figure out what happened.

Does anyone have any ideas or suggestions to help shed some light on what could have happened with an app update to cause data loss?

EDIT: More details: I've checked every archive submitted to the App Store and both use the Production environment for iCloud containers using the same ubiquity container and the same rights. I'm stumped!