Where did the content of my Downlods folder disappear to?
Time Machine backs those files up. Have you checked your backup?

If you don’t have a backup, you might need to follow any of the several questions here about software that looks for deleted files and folders and shut down the Mac immediately to prevent further data loss from overwriting free space with new files. 


How to recover a deleted file on Mac OS X?


If you don’t care about recovery of files, get a backup of what you still have and then boot to Recovery HD and check the disk for errors before recreating the folder.