Oops, probably you didn't untick the Filename, Filename (name) and/or Filename (path) tickboxes when you used the cleaning tool.
DVD videos are only referenced through the special "DVD files on a hard drive" structure. That's why there is the additional ";1" filename extension. MC can't actually rename or move the various "DVD disk files".
Before doing any big changes like that you should always rehearse the procedure with one or a few test files (or "DVD videos in a folder" in this case).
There may be a few ways mass fix the problem by using an external tool for naming the folders back to VIDEO_TS ...* and then using the internal tools creatively for restoring the original filenames or by simply importing the files as new since the metadata should be stored in the sidecar files. In order to give specific instructions I would need to know more about your file naming system. Perhaps you could upload a couple of sample sidecar files.
Actually, are you saying that you don't have a recent library backup file? I always create a new backup file before any big tagging or renaming tasks and another one immediately after the operation if everything went well.
In addition, I also store my video metadata in MPL files that I export to the roots of my video folders. Sidecar files are good for individual files, but MPL makes possible to do externally "find and replace" operations that fix or change all included files.
* EDIT: ...or are the original VIDEO_TS folders still intact? That would make the fixing process easier.