Previously, I was able to see each file in the prefetch folder. Now they don't appear at all and they are not hidden files. What gives?

These are files created by the system for it's own needs, sometimes they are not saved and deleted when system shutsdown
But often they will stay in that folder - these files are created as needed for the system, typically only 16kb

To be honest, really don't need to worry about these unless you are looking for something specific to do and most times the system will not let you delete them as they are in use by the system