If you suddenly notice that Media Player lost all your files, it means that tracker couldn't handle all the changes and is probably re-indexing your files, so don't worry. You can try turning your phone off and on again. You can also check the status of tracker (the service that tracks all files and indexes them for e.g. the Media Player) by running tracker-status in the terminal as a normal user (not as root). If there is anything fishy going on in the output, please report back.