Something else on your PC moved the files by the sound of it.
If the files have actually been moved, and you aren't just looking at a different View in MC. In fact, what View are you using in MC to see that the movies are in a different folder? If MC didn't move the files, you wouldn't see them in a normal view, but only in the Drive & Devices > Explorer View, as they would no longer be imported into the MC Library, depending on settings. Also, for movies MC would have created Sidecar files to store extra metadata. Where are those files now, back in the original directory, or in each new directory?
Certainly, the MC
Rename, Move, and Copy Files (F6) could do that, but if it did, MC would still have all the movie information.
Do you still have iTunes installed, and did you open it or let it update?
Have you been using Windows Media Player, and letting it organise files?
Do you have any other media software that you have used in the past, or installed a trial for, and haven't uninstalled?
Unfortunately, if the files have actually been moved to another folder of their own, you can't just restore a MC Library Backup to fix it. But then having each movie in its own folder is Best Practice, IMHO, and is how I store my movies.
What you can try is to change the Auto Import settings to "Update for external changes" and uncheck "Ignore files previously removed from library", just temporarily, then manually run Auto Import. MC may then find the movies in their new location and associate the metadata it had previously with them, including the Cover Art.