iCloud "deleted" all Documents and Desktop files, where are them?

You’ll have to wait for the uploading to complete, then turn off the functionality. Here is what happens at this point:

What happens when you turn off Desktop and Documents

When you turn off Desktop & Documents Folders, your files stay in iCloud Drive and a new Desktop and Documents folder is created on your Mac in the home folder. You can move files from iCloud Drive to your Mac as you need them, or select all of your files and drag them to the place you want to keep them.

What happens when you turn off iCloud Drive or sign out of iCloud

If you turn off iCloud Drive or sign out of iCloud, a new Desktop and Documents folder is created in your home folder. You also have the option to keep a local copy of your files that are in iCloud Drive. If you keep a local copy of your files in iCloud Drive, they're copied to a folder called iCloud Drive (Archive) in your home folder. You can move any files that were in your iCloud Desktop and Documents to your new local Desktop and Documents.

Source: Add your Desktop and Documents files to iCloud Drive - Apple Support.

Migueldlm wrote:

I tried to disable the option hoping to find my files there again, but they are not restored there, however they are still being uploaded to iCloud (more than 40GB... it would take days!).

Not days, more likely ~ 10 hours (assuming 1 MB/s upload speed). So let it run overnight, and you might also set your Mac to not allow the computer to sleep while this is happening (ok to let the display sleep).