This almost caught me too - they've recently added the Download folder to the Disk Clean-up tool in Clean-up system files. So, either don't have any files in the Download folder or de-select that option in the tool.
This did catch me :(
The Download folder has been added to Disc Clean-up only since windows version 1809; and usually I tick off all the boxes - which is what I did again this time.
So I lost all contents in my download folder!!!
Tried to recover the contents using Shadow Explorer - but all the .pdf's, .mp4's, … which were recovered are corrupted!
All "recovered" files are non-viewable and non-playable.
This is not an error or a miss on the part of Microsoft. I am certain I will not be the only person to lose files from the Download folder.
Why did Microsoft not warn us that the Download folder is now included in Disc Clean-up????
And so much for all those reviews of version 1809 - none mentioned the new "feature" of having the Downloads folder in Disk Clean-up (let alone the data deleted only upon installing 1809).