Try switching the USB mode to MSC. Your computer can only see files loaded in one mode at a time. Maybe at some point your player was set to Auto Defect mode which would allow it to connect in either MTP or MSC without your knowledge.
If you’re not usiing DRM-crippled files why are you using MTP mode? That’s the only reason one would need to use this mode, and MSC is much less troublesome.
