Hi Stephen, I just went 3 furious argumentative rounds of frustration with the Lead Trainer at my local Apple Store.
My complaint is the same as yours.
At the time of Upgrade / Migration to Sierra, all of the dialog boxes indicate that our Documents Folder would be "synced" or "mirrored" to iCloud.
I agreed and checked the box for "yes", this sounds good.
Truth is, that the set up process is PATHETICALLY, RIDICULOUSLY, INFURIATINGLY misleading to the point of just being outright B**L S**T.
The facts are....
1) NOTHING is "synced" or "mirrored" at all. This languaging with the word "sync" is a total BS lie. NOTHING is being "synced".
2) What actually happens is that you local Documents Folder on your local hard drive is...
A) renamed "iCloud Drive (archive) (the name may vary on other machines)
B) the folder is moved to a new location (on mine it was in my Home Folder)
C) your documents folder and contents, is uploaded to iCloud
D) all Finder / OS connectivity to your old Documents folder is severed (in terms of it being recognized any longer as the Documents folder)
E) ALL your Documents from this moment forward, live ENTIRELY 100%, PERMANENTLY, in iCloud. They are not "synced". They are not "mirrored". They are literally MOVED and relocated to iCloud.
3) ALL ability to backup the Documents Folder moving forward is 100% completely eliminated, because your Documents no longer "live" on your hard drive. They are 100% in the cloud now.
4) ALL accessing of ANY document moving forward is 100% cloud based. Want to edit a file? Click on it and it will download to your machine from the cloud for you to work on. When youre done and save the document, it will be 100% saved in iCloud and NOT on your machine.
5) Your ability to access ANY and ALL of your files moving forward will be 100% dependent on the reliability of and access to an internet connection, combined with the reliability of Apple's iCloud system. (which from it's inception has been fraught with reliability issues for YEARS.) No internet connection?.... then NO access to any documents EVER.
6) Want to feel safe that your documents are backed up? Too bad. ALL faith, confidence, trust, reliability in the system and your ability to access or backup ANY and ALL of your files is 100% dependent on Apple.
7) Feel like trusting Apple iCloud with 100% of EVERYTHING you have ever written or created for the last 40 years is putting too much trust into one fragile, unreliable basket and you would like to reverse the process, turn off Documents and Desktop in iCloud, and get your Documents folder back local? Good luck.
Online instructions say, "just uncheck the Document and Desktop" check box in iCloud System Preferences and your Documents folder will be downloaded back to your desktop drive. This is 100% Bull Sh*t.
I spent an hour yesterday at my local Apple Store talking with an arrogant woman who boasted about being the Lead Trainer who knew the answers to everything. She didn't have a clue about how to reverse this. She just kept throwing out lame guesses. I've also talked to 3 different Tier 2 Senior Support people on the phone. None of them knew how to reverse this.
So far I haven't found anyone, online or Senior Apple Support, who have any clue how to reverse this process. There are a few online loud-mouths who will insist they know how and a few more Apple people who will throw out lame guesses, but the truth is that so far, "nobody" with any credibility seems to know how. My tests of the loud-mouths assertions have not shown results that match their claims.
Here is one very important consideration.
The local Documents folder on a desktop machine running OSX (macOS) isn't just the same as any old folder with any old name, but in this case just happens to be named "Documents". NO.
The Documents Folder, (before upgrading to Sierra, totally screwed everything up) was fully integrated in more complex file/recognition ways than just a regular folder. Just as you can't call any folder "System" and then it magically becomes the System Folder, simply because you named it such, you can't just name any folder "Documents" and have it magically become the OS recognized Documents Folder, just because you named it such.
So, reversing the process and taking the now-named "iCloud drive (archive)" folder, changing the name back to "Documents", and dragging it in the Finder back into the Home Folder, DOESN'T WORK.
We shall both need to keep reading these forums in hopes that SOMEONE who actually knows something at Apple will respond.
(Feeling angry and misled about this "iCloud Documents" issue? Search for my other post about how upgrading to Sierra will render ALL the backups that you have EVER made using Time Machine, useless, unreadable, garbage, because with Sierra, Apple changed the entire file system from HFS+ to their new format APFS. Sierra can not recognize or read ANY backup file made with the previous file system HFS+. Do you think your data is safe because you backed up? Sorry. All your backups, (pre-Sierra) are all useless, unreadable, junk. Read my other post for details.)