For Kodi clients you can follow what I posted here for dumping the cached artwork
That post was also dumping the local video database so since your using MySQL you don’t need to delete the MyVideos116.db file. You will need to drop the <name>116 in MySQL. There is various ways to do it. I personally use HeidiSQL which with that one it is just a matter of connecting and then right click on the db name and select drop.
Best practice here would be (after deleting all empty files) to stop Kodi on all your clients, drop the db, then delete client cache, then start Kodi again, set scrapers, scan library.