When your player is connected to your computer under USB MSC mode (set under the player’s Settings/USB Mode), your computer only sees the files that had been transferred to the player when the player was connected under MSC mode. Likewise as to MTP mode. Regardless, all the files show up and are playable on your player, under whatever USB mode setting.
Could it be that the files you can’t see were transferred to your Clip under MTP mode, and your computer isn’t showing them because you now are under MSC mode? Note that if you were under Auto mode, the Clip will try to use MTP mode first.
If that’s the case, you can reformat the Clip under its settings and start over. Note: this will erase your content on the Clip. Otherwise, find a PC you can connect to under MTP mode and connect; transfer your content back to the computer; disconnect and reconnect under MSC mode; and transfer your content back to your Clip.
Hope this helps–