Coding on PC is one of my hobbies, so I was curious to see if I could bash something together. I've got it working to where you click on the program, choose the folder location of your files and it finds all matching file names (no folders) in the folder and zips them into their own zip folders.
You will probably need Administrator privileges on your PC.
It needs more testing, a user interface, progress bar, and some confirmation prompts, but I could private message you a download link and instructions if you want to give it a try.