Sometimes iCloud Drive will remove files to reclaim storage space on the local device.
 

If your website folder isn't displaying correctly in the browser, the first thing to check is if one of your files was offloaded from the device:
 

1. Check the folder in iCloud Drive using the Files app (on iOS) or Finder (on macOS)
    
2. If you see the cloud symbol with a down arrow, you need to download the file:

• On iOS, tap & hold on the file until you see the menu, then tap Download
• On macOS, click on the cloud arrow icon

After the files are downloaded, refresh the site in the browser.