iPhone 6s owners report losing messages, recent calls when restoring from iCloud
Some people picking up a replacement iPhone 6s are finding that their Messages and Recent Calls data is missing after restoring from iCloud, according to numerous complaints.

The issue is the subject of multiple threads at Apple's support forums, and has been verified by AppleInsider. Anecdotes hint that even some people within Apple may have suffered the problem, and that in some cases people are losing additional data such as Health statistics or Safari browsing data.
The root of the glitch is uncertain, but may be connected to the original devices being updated to iOS 9.0.1 or later, and the replacements having iOS 9.0. Others have suggested simply that iCloud is pushing out corrupt backups.
Regardless, one user-proposed solution is making sure both the new and original phones are updated to iOS 9.1, running a fresh backup of the original device, and then resetting the second phone to factory settings. Only at this point is it theoretically safe to restore from iCloud on the new hardware.
Possibly simpler is relying on local iTunes backups, especially since the original device may be missing or non-functional.
Apple support representatives have told customers that the company is aware of the issue and working on a solution, but no timelines or official workarounds have been announced.

The issue is the subject of multiple threads at Apple's support forums, and has been verified by AppleInsider. Anecdotes hint that even some people within Apple may have suffered the problem, and that in some cases people are losing additional data such as Health statistics or Safari browsing data.
The root of the glitch is uncertain, but may be connected to the original devices being updated to iOS 9.0.1 or later, and the replacements having iOS 9.0. Others have suggested simply that iCloud is pushing out corrupt backups.
Regardless, one user-proposed solution is making sure both the new and original phones are updated to iOS 9.1, running a fresh backup of the original device, and then resetting the second phone to factory settings. Only at this point is it theoretically safe to restore from iCloud on the new hardware.
Possibly simpler is relying on local iTunes backups, especially since the original device may be missing or non-functional.
Apple support representatives have told customers that the company is aware of the issue and working on a solution, but no timelines or official workarounds have been announced.
Comments
Maybe its just me, but I'd never consider content of a messaging app to be a permanent data store.
This concerns Health data and other things as well.
My wife was using my 5c (on iOS 9.1) when suddenly the phone completely deleted itself. No idea why or what she did (if she even did anything) but I restored from iCloud and definitely I was missing many emails.
No problem since and when I upgraded to my 6s+ using iCloud to restore it happened flawlessly. So my conclusion is that it's an issue with iCloud and NOT the 6s+
Another reason I don't back up to the "cloud".
No it's just every thing immediately hits the internet these days, shows up all over Twitter, Facebook Apple rumor sites, etc, etc. etc.
I thought that losing messages was normal when restoring with iCloud. My understanding is that iCloud does not back up everything, and you will lose some data when restoring from iCloud. That's one reason why I've always used iTunes backups when restoring.
I experienced this problem. It wasn't just messages, data in some other apps got lost as well. I had created an iTunes backup at the same time, so I restored with that.
This is a regression... used to work.
This is why I always make a back up on my computer, those seem to be far more solid backups then icloud, plus I not willing to keep paying apple for cloud storage when I have Terabits of storage at home.
I've never had any issue with this. All my messages are compl
I've got every message I ever sent since the iPhone 3GS backed up and it's been useful several times to confirm the dates that something happened or correct a misunderstanding. My messages app backup is currently 11GB. I always back up to the computer - but i don't think anybody who backs up to iCloud should expect their messages to randomly disappear. They should be able to rely on a secure and reliable backup: There's obviously a bug that needs fixing.
/s
Bullsh**t! That's not at all general knowledge - nor is it an actual requirement. If it *were* a requirement, the restore process itself would warn the users or even insist upon an upgrade before allowing the restore to happen.
People that call other people stupid when they're really not - are the stupidest people in the world!
Did 9.1 to 9.1.
Also you can't use back up from iOS 9.1 to older version iOS, they are not compatible!
I backed up perfectly fine. 9.1 to 9.1. Everything else restored but my texts, call history and the data of some apps.