Some documents missing in icloud

Sorry but an confused.

The missing documents were located on the Internal Drive and where being Synced to iCloud ?

If the files are missing from the Internal Drive and are missing from iCloud too

Bad news - unless the user has a Time Machine Backup from before the documents when missing - they are gone.

Link below may help to restore specific files using TM Backup

Restore items backed up with Time Machine on Mac - Apple Support (CA)

The user may or may not have a complete picture of how iCloud works

iCloud is Only a Conduit to have files on Both the Internal Drive and also on iCloud.

When an Application is used and assigned to Sync with iCloud, changes made on the Local Copy will be automatic be reflected with those changes.

This will allow the user to see and access that same Changed Document from any other device that is signed into and using the Same Apple Apple ID.

iCloud is not designed and intended to be a Storage Space to Archive and Off Loan fees in order to make space on the Internal Drive.

That specific usage & practice is best used by an External Drive and / or some Other Cloud Based Storage Service.

Q - " Wasn’t aware my hard drive docs would be compromised "

A - In what exact way is the hard drive believed to be compromised - Details please.

A - Specific to Big Sur macOS 11 and above. The Operating System resides in a Sealed and Read Only Volume that can not be opened by the User.

A - The only compromise would only be from within the User Admin Account of this computer and not the entire Operating System

Then have a few suggestions ;

1 - Get Support Choose a product and we’ll find you the best solution.Start now and open an Apple Support Ticket as they are Apple Employees to deal will these types of issues . 

2 - Product Feedback - Apple and make it known to Apple regarding this ongoing issue 

Good Start in trouble shooting thus far 👍

In System Setting >> Your User ID >> iCloud Drive

Click on iCloud Drive which will open another screen like in 2nd image

Click on " Apps Syncing with iCloud Drive " >>> " Options "

Now, in the next 3 images are listed all the Applications that are sent to Sync Documents

Make sure all relevant categories are enable

First image

Second image

Third, Fourth and Last

Then suggest logging into www.icloud.com and sett if the missing documents are appearing there.

Also, when in iCloud, check the Recently Deleted