Q: Notes sync inconsistently across multiple devices and web portal

To start, I just want to be clear that I have a very throughout understanding of iCloud and Apple products. I am a former Apple Genius and have spent a great deal of time trouble shooting this issue. I believe that this is only something that can be resolved by Apple engineering, however, I am open to any suggestions. I'm going to detail a great deal of information here. Also note that I have contacted Apple Care and gone through several troubleshooting steps with them as well, with no resolution. I greatly appreciate any discussion on the topic that can assist me in finding a solution. More importantly my hope is that Apple will take notice of this issue because I can't seem to convince anyone to escalate this to engineering.

I can't say for certain when this issue began. I only noticed it within the last month or so, however I suspect that it may have arose after the upgrade to the new version of Notes in El Capitan and iOS 9. I can't be certain though. The issue appears to be that there are two separate instances of Notes syncing within iCloud. That's really the best description I can offer based on the behavior I am experiencing. The short of it is when I access Notes from my iMac and from iCloud.com I see one set one of notes that are synced. When I access notes from any of my iOS devices I see a completely different set of notes some of which are older versions of the notes I see on my iMac and iCloud.com and some are new ones that I have added recently. But they are all the same notes across all the iOS devices and they sync properly. They just don't sync to the iMac or to iCloud.com which both sync properly with each other but not with the iOS devices. Interestingly enough all other iCloud apps sync across all devices and iCloud.com as expected. It is one of the strangest issues I've encountered with iCloud sync.

The following are all the details involving this issue:

First let me start with hardware. I have the following devices syncing to this single particular iCloud account & Apple ID.

2010 27" iMac running the latest version of El Capitan with this account set up as the primary iCloud account and using iCloud drive

13" MacBook Pro with Retina running the latest version of El Capitan with this account set up as the primary iCloud account and using iCloud drive

iPhone 5 with this account set up as the primary iCloud account, is running the latest version of iOS 9.3 and has iCloud drive turned on

iPad Mini with this account set up as the primary iCloud account, is running the latest version of iOS 9.3 and has iCloud drive turned on

iPhone 4 with this account set up as a secondary iCloud Account and running the latest version of iOS 9.3

iPhone 6 with this account set up as a secondary iCloud Account and running the latest version of iOS 9.3

iPhone 6+ with this account set up as a secondary iCloud Account and running the latest version of iOS 9.3

Each of these devices did at one time all sync properly. Additionally I am using all iCloud Apps and services across all devices where permitted. As secondary accounts only some Apps and services are available. Once I noticed the situation I immediately removed all the devices from the iCloud account in the hopes that this would resolve the issue. If you were to login to the account right now via the web portal it would read "No Devices" under iCloud settings.

After removing all devices I then proceeded to iCloud.com and logged in to see which version of notes were available. It is still the same version that is syncing with the iMac. We will refer to these as old notes. I then configured the iMac to work with the account and it again synced the old notes. Finally I configured the iPhone 6+ with the account and it again syncs the new notes. Everything is just as it was before I logged all the devices out. I've since removed each of those devices and the account is sitting idle with no devices attached. I've spoken with Apple Care about the issue and the only thing that they've recommended at this time was to enable iCloud drive on all devices. iCloud drive is enabled on all devices where applicable and the issue still persists. I can also assure you that I am not using a different iCloud account nor am I storing Notes locally to my internal storage. I can confirm this because if I create a new reminder on any device it updates as expected across all devices including the iMac and iCloud.com. Also, because I can see that I am accessing the correct account from the Notes App.

I'm completely out of ideas except to create a brand new iCloud account which seems wasteful. Hopefully someone out there has a solution!