Files (songs) placed onto the player in one USB mode (MTP or MSC) are not visible on the computer while the player is connected in the other mode.
Firmware updates often re-set the device back to the default (MTP). If you previously put songs on (before the f/w update) in MSC mode, and the player got switched back to MTP from the update, that would explain why you can’t see those songs now, but when you dis-connect your player, they are in the menus.
The simple answer? Change your USB mode back to MSC (SETTINGS > SYSTEM SETTINGS > USB MODE). Now your former songs will be visible, but the songs you recently put on (after the f/w update) will not be.
The longer answer? Pick a mode that is best for you. Connect your player in the other mode. Delete all the songs. Un-plug the player, wait for the database refresh and switch to your preferred USB mode. Re-connect to your computer and re-load all those same songs again. Now everything will show on your computer (unless the player somehow gets switched again).
Here’s a primer on MTP & MSC mode to help you decide which is best for you.
Oh yeah . . . just to confuse you even more, there’s also an AUTO setting. This defaults to MTP most of the time. I’d advise choosing one or the other and not depend on the AUTO setting.