If you select a folder from within MP3tag then you see only the folder itself but not files in it as the only object that can be opened is a folder. And if there are not further folders in a folder then the last folder appears empty.
If this does not match your observation, then please tell us step by step what to do to reproduce it.
As this is an action performed by the OS - where do you see the role of MP3tag? If MP3tag is not running, it is not very likely that it blocks the files.
Do you get any error messages?
You would have to supply more details about the differences between files that work and others that don't.
Also, you would have to make sure that your mass storages are still in working order, you have sufficient access rights, the files that you edit are not corrupt and so on.
Do you use any synchronization software?
But as I doubt that this has actually anything to do with MP3tag and the use of MP3tag is only coincidental with your troubles I do do not think that I can really help you.