It is really weird that so much of the documents are missing from this level of folder…any ideas about what I did wrong? If this happened when I cleaned up the desktop why are the parent folders still in place but all the contents gone?

I am perplexed...
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1. The screenshot you took is a little too small for me to make out some of the details. However,

2. It looks like you are looking at an iCloud Drive folder. I have seen this behavior before. Check to see if you have an iCloud Drive “Archive” folder in your home folder and if you do, check to see if the documents you are looking for are in the Archive. This can happen when iCloud Drive is disabled then re-enabled.

3. Cleaning the desktop would not effect folders that live in other places. Even if you had aliases pointing elsewhere and tossed out the originals, you would still see the abandoned alias file. So that’s not what happened. I’m guessing this is related to iCloud.

4. Check at iCloud.com to see if you can locate those documents via a web browser.

5. Do you have a time machine backup that we could use to recover these files. I LOVE time machine and it usually saves the day.