Sorry nothing seems to be working for you. Frankly, I can’t understand it either. There’s one more thing you could try; re-applying and/or updating the firmware. Formatting would wipe the memory clean, so I understand you hesitance in doing that, but re-installing or updating the firmware wouldn’t affect the files on it at all.
You can find the latest firmware versions here. You’ll have to check whether you have a v1 or v2 version (if you don’t already know) so you download and install the correct one for you hardware configuration, but that’s easy. Go into Settings > System Settings > Info and read the top line (which is the firmware version currently on the player). If it starts with a 01, you have a v1 model; if it starts with an 02 you have a v2 model. Click the link that says All Regions (don’t bother with the Updater) and follow the manual installation instructions. Basically, you download the .zip file, extract it and save it (your Desktop is a convenient location) and then drag & drop it to your player (connected in MSC mode).
Be aware though that updating the firmware will revert the USB setting back to Auto Defect, so after you will have to choose either MTP or MSC manually. You may need to do this anyway to look for your missing files.
Good luck . . . let us know how it goes.
