For accessing your Android device via USB in "File Transfer" mode your computer uses the MTP protocol. This protocol allows to list and read/write the files from/to your device.
What most people don't know is that the MTP protocol does not show the content of the file-system. Instead it uses the Android MediaStore Database (an SQLite database) which is populated by the Media Provider, a special daemon running on Android (app package name:
If you create a new file/directory or delete something without notify this daemon the database and the file-system are out-of sync and you end up that you can see files already deleted or can't see existing files.
You can force the Android MediaStore to refresh it's database, e.g. via ADB command-line (source):
adb shell am broadcast -a android.intent.action.MEDIA_MOUNTED -d file:///sdcard
There are also a lot of apps that can force a rescan of the sd-card.