How can I prevent iCloud folders and files from suddenly vanishing?

What caused all my folders to vanish on the desktop then end up empty when I attempted to put them back?

After doing the three "just simply" suggestions in checking why my files and folders suddenly vanished - go to your icloud.com, check the recently deleted, restore - blah blah blah, nope. Didn't work.

Spent over 5 hours yesterday going into the Time Machine, finding documents, files, folders, repopulating folders. 10 Word documents vanished. So... aside from the pat answer as to what to do when they disappear - which didn't solve the issue - what is the official reason that folders and files just vanish from iCloud?

We've got over 15 years of files, photos, we're marketing a live theatre production right now, we have pitch letters saved, samples, POOF! Gone. What's the answer? Fortunately I was able to get about 95% back from the Time Machine. And I guess I have to pay for Carbonite now since this is unreliable. I've got "optimize" set. What's the reason though? Oh... and 200gb of "space" and the computer is 256gb, the other shared computer is 500gb, combined they use 420gb and the STORAGE for this 256gb says it's using 12gb of space though all files are supposedly in the cloud. Any thoughts?

[Re-Titled by Moderator]