Are you saying that you hole punch every page for every mystery shop? I've found that to be extremely time consuming and messy. I know that some shoppers use several clipboards, but I find that things fall out of them.
I recently started putting plastic files in loose-leaf binders for some types of projects and liked them so much that I am doing that for all my work. I like large paper clips rather than the tiny ones. What I am doing is putting each shop, and my merchandising assignments, too, in a plastic sheet that has the front part of the plastic going only halfway up. It is easy to remove and put back the sheets. They don't fall out and they don't get lost. I can have one plastic file for instructions that haven't changed, and the one in front will contain the current assignment.
The only thing I'd warn about is having the mystery shopping ones easily seen if in a store merchandising. If you drop your loose-leaf binder, you'll likely have to buy a new one because the clips will not work properly after that.
You can organize them any way you want, by day of the week, even by using different-colored plastic. You can even change them if what you are doing doesn't work for you. The plastic organizers themselves aren't cheap but they last as long as they aren't overstuffed.
I tried an expandable file with a top that closes, but it is too easy for things to get lost in there, and there is no place for unusual assignments. There are never enough sections for occasional assignments from some of the many MSC's we have to register with.
If you need one set, for example for an audit, you can put it in a clipboard. Then put the finished paper back in the plastic for the ride home.
Since I also merchandise, I have binders for two different companies and then one for everything else, including mystery shopping. There are some merchandising companies that I rarely work for so their file is in the MS one. If I were still a full-time mystery shopper, it would be a little different.
Maybe you can find something in my narrative that will help you.