This is just a guess, and I might be way off, but I wonder if Frank is using comic book reader software to read this, or if he's somehow opening the file as a folder in Windows Explorer or compression software like Winzip or 7zip? Just because re-ordering files like he describes sounds like something Windows Explorer has done for me.
Even if you're not intentionally using Winzip or 7zip to open the file, if you accidentally changed your settings so that one of them is the default software Windows goes to for opening CBRs and CBZs, it will automatically open the file with that software if you double click the file. You can change that setting in Windows' control panel.
Link to the book:
Firefly Complete Collection