Uploading Documents is a Migration not a Sync Although they are related

When you select the Documents folder under iCloud Drive in the Sidebar, are they there?

When you turn on Desktop and Documents in iCloud Drive, nothing is ever moved. There is only an upload. Hard links to the files are created to make it appear they are someplace else, but the original storage is not affected.

Finder does hide the Desktop and Documents folders and shows them in iCloud Drive. While uploading will stall when you don't have enough storage on iCloud Drive, all of the files should still appear there because they are hard linked. Are they not showing up in iCloud Drive?

If you disable Desktop & Documents in iCloud settings, it should ask if you want to copy them to your Mac. That will make them appear in an iCloud Archive folder in your home folder. Again, nothing is moved. Just hard links are created.

The files and folders are hidden in some way or renamed so as to not interrupt the upload/migration preventing corruption.

That isn't why they are hidden. There really isn't any migration. The files are hard linked into the Mobile Documents folder. The original files remain in the Desktop and Documents folders. When you turn it off, the hard links are removed from the Desktop and Documents folders. The files are still located on disk where they were originally and the hard links in the Mobile Documents folder point to that original storage location.

There is enough storage and the doc folder disappeared and never came back. Remember they never finished uploading. They are not going to be in the cloud at all and should be sitting somewhere waiting for the upload.

No, they won't be actually in the cloud, but it will still appear that all of them are there as I explained. Hard links to the files are created in the ~/Library/Mobile Documents/ folder which is what selecting iCloud Drive shows.

I even turned the option on and off to get them to upload again but it only uploaded my current empty doc folder so the archive folder created from turning off the sync does not have them. Again makes sense because they never completed the upload/migration. There has to be a .backup or .sqlite file where the info can be retrieved. Basically I know the folders are renamed into something to do the upload/migration.

When you first turned it off, it didn't ask you what to do? Did it not offer to Archive them or leave them in iCloud? What did you choose?

If you turned it off and left them on iCloud, they should still appear there. And they would have been in the hidden Desktop and Documents folders. However, turning it on again would have indeed synced your empty folders because that is what it does when you turn it off. It shows the formerly hidden folders and removes all of the hard links in them.

The hard links should still be in the Mobile Documents folder.

You may have suffered some irrecoverable glitch, but what you think happens with iCloud Drive is not what actually happens.

I would doubt that most of the people working Apple Support do not understand what happens, either.

Obviously chose keep a copy.

There isn't an iCloud Archive folder inside your home folder?

Yes but the files that never finished uploading were not there. That makes sense to me.

It may make sense to you, but that is not what happens. I told you what happens.

I'm saying the hard links are there but not finalizing.

There is no such thing. They are created instantly. They are merely pointers to the storage location on disk. They aren't finalized in any way. There is no waiting for the upload to complete. The upload begins when the hard links are created.