Missing music in Android File Transfer, where did it go?

[AC Question]

Missing music in Android File Transfer

I add a podcast to my phone every week via Android File Transfer. Today I go to transfer it over and half my music isn't showing up in the proper folder. If I navigate to it in Es File Explorer on my phone the music folders are all there. If I try to play them, they play fine. But navigating to the directory in Android File Transfer on my computer, half of them just aren't showing up. Just complete band folders are podcast folders aren't there, even though they are...

Nexus 6
Android 6.0.1