iCloud Restore for iPhone 6s - Missing Messages/Recent Calls Missing
Day one my wife and I got our new iPhone 6s (with iOS 9.0). We did an iCloud restore from our iPhone 5s with iOS 9.0.1 and it was successful bringing all our data including Messages and Recent Calls. The phones were then updated to iOS 9.0.1. Everything was working fine...
My phone had an issue which ended up getting me a replacement iPhone 6s (iOS 9.0). From here I tried restoring from the past iPhone 6s (with iOS 9.0.1) iCloud restore. Unfortunately, Messages and Recent Calls did not come over from the past iPhone 6s backup and I even tried various of the iPhone 6s time stamped backups. I also updated the new iPhone 6s to 9.0.2 and still no difference with the restore. It wasn't until I reverted back to my iPhone 5s backup (iOS 9.0.1) that it would bring the Messages and Recent Calls over. Note that the inclusion of the Messages and Recent Calls is evident immediately after the initial restart from restore (when the phone starts downloading apps). This has me worried going forth and here is why!
I've done a new backup and a little digging. I've noticed that both my new backup for the iPhone 6s and wife's are both smaller than our iPhone 5s backup was. Example for my device backups: iPhone 5s: 18 GB, iPhone 6s: 17.1 GB. Note that this seems backwards as if there was any difference for whatever reason, I would imagine that it be on the larger resolution device. Also, this difference in size would seem reasonable for not including Messages (includes messages, videos, audio, etc.) and Recent Calls. There may even be other data that this did not bring over as I did not see it benefit in losing years of messages for a week of new data, i.e. I did not research the loss to the full extent.
Has anyone else experienced this issue recently with an iPhone 6s or maybe there is a known issue I just have not stumbled across.
iPhone 6s, iOS 9.0.2